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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/paml">Debian Med / paml</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99">cdd16ab7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-10T17:54:43Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.9j+dfsg</pre>
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<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#603f97d72b27a59317d9825dc0d317754f294f0e">
doc/pamlHistory.txt
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<li class="file-stats">
<a href="#32612ead0c63388da55f4d32fdd68a1e6abe9f05">
<span class="deleted-file">
−
doc/pamlHistory.txt~
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<li class="file-stats">
<a href="#36f02a818879b7054d2e8f2e5cd2c9bf68a424e9">
<span class="deleted-file">
−
paml4.9i.tgz
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<li class="file-stats">
<a href="#960e07dc156e2297a21a85a1fcb9d2a781c8b3e5">
src/mcmctree.c
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<li class="file-stats">
<a href="#92dbb696e9045a01875b9f9494678f0dfc5a05cd">
src/paml.h
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<li class="file-stats">
<a href="#a285bdff300c2b5227532ac230a53690458860a1">
<span class="deleted-file">
−
src/pll_avx.c
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<a href="#6c4ed75b16bf498d6c4b6a1032a8793efc182652">
<span class="deleted-file">
−
src/pll_sse.c
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<li class="file-stats">
<a href="#764a5fe9e31ebe9fe8818a076331ce42ae7456dc">
src/tools.c
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<li class="file-stats">
<a href="#a38117fbc1bdd77b43c1c50e6dda570e0ba75c72">
src/treesub.c
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<h4>Changes:</h4>
<li id="603f97d72b27a59317d9825dc0d317754f294f0e">
<a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99#603f97d72b27a59317d9825dc0d317754f294f0e"><strong>doc/pamlHistory.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,31 @@ discussion site</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">https://groups.google.com/forum/#!forum/pamlsoftware.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Version 4.9j, October 2019</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">(*) mcmctree, initial values have ages that are too old, exceeding max</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">bounds. In theory bounds in mcmctree are always soft so that the node</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">ages will move to the area of posterior mode when burnin is long</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">enough. In practice the poor starting values are problematic and</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">requires long burn-in. I have rewritten the code for generating</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">initial values to respect the min and max bounds specified in the</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">fossil calibrations.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">(*) codeml, clade labels in the tree file. A bug introduced in 4.9i</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">caused the clade labels ($) to be ignored. This affects the branch,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">branch-site and clade models. If your tree has branch labels (#) only</span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">and no clade models, everything will be fine. If you have used the</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">clade label ($) in the tree with or without the branch label (#),</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">either the program will abort or the results will be incorrect. The</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">clade label ($) is supposed to label all branches in the clade as well</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">as the branch itself, but all clade labels in the tree are ignored in</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">4.9i. Earlier versions are correct.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Thanks to Yonghua Wu for pointing out the bug.</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Version 4.9i, March 2019</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">(*) mcmctree: I have added an option (duplication = 1) for dating a</span>
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<li id="32612ead0c63388da55f4d32fdd68a1e6abe9f05">
<a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99#32612ead0c63388da55f4d32fdd68a1e6abe9f05"><strong>doc/pamlHistory.txt~</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">History</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">fixes</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">PAML</span> <span class="p">(</span><span class="n" style="color: #333;">Phylogenetic</span> <span class="n" style="color: #333;">Analysis</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">Maximum</span> <span class="n" style="color: #333;">Likelihood</span><span class="p">)</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="mosel"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Ziheng</span> <span class="n" style="color: #333;">Yang</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="mosel"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="mosel"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">find</span> <span class="n" style="color: #333;">problems</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">questions</span><span class="p">,</span> <span class="n" style="color: #333;">please</span> <span class="n" style="color: #333;">visit</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">PAML</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">discussion</span> <span class="n" style="color: #333;">site</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">google</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">forum</span><span class="p">/#</span><span class="c1" style="color: #998; font-style: italic;">!forum/pamlsoftware.</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2019</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="mosel"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">:</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">option</span> <span class="p">(</span><span class="n" style="color: #333;">duplication</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">dating</span> <span class="n" style="color: #333;">a</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="mosel"><span class="n" style="color: #333;">tree</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">speciations</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">gene</span> <span class="n" style="color: #333;">duplications</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">nodes</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">share</span> <span class="n" style="color: #333;">divergence</span> <span class="n" style="color: #333;">times</span><span class="p">.</span> <span class="n" style="color: #333;">Nodes</span> <span class="n" style="color: #333;">sharing</span> <span class="n" style="color: #333;">ages</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">identified</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">labels</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="p">#</span><span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="p">....</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">yet</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">update</span> <span class="n" style="color: #333;">the</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">document</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">specification</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span><span class="p">.</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="mosel"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">TipDate</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">written</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">locus</span> <span class="k" style="font-weight: 600;">or</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="mosel"><span class="n" style="color: #333;">partition</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">never</span> <span class="n" style="color: #333;">worked</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">loci</span><span class="p">/</span><span class="n" style="color: #333;">partitions</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="mosel"><span class="n" style="color: #333;">edited</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">works</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">partitions</span><span class="p">,</span> <span class="n" style="color: #333;">some</span> <span class="k" style="font-weight: 600;">of</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="mosel"><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">molecular</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">others</span> <span class="n" style="color: #333;">morphological</span><span class="p">.</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="mosel"></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">estFreq</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">codonFreq</span> <span class="p">=</span> <span class="m" style="color: #099;">6</span> <span class="p">(</span><span class="n" style="color: #333;">FMutSel0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">FMutSel</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">working</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">g</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">h</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="mosel"><span class="n" style="color: #333;">now</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">uses</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">observed</span> <span class="n" style="color: #333;">codon</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">frequencies</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mutation</span><span class="p">-</span><span class="n" style="color: #333;">selection</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">usage</span><span class="p">.</span> <span class="n" style="color: #333;">Instead</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="mosel"><span class="n" style="color: #333;">estimates</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">frequencies</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">likeihood</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">what</span> <span class="n" style="color: #333;">the</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="mosel"><span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">estFreq</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">does</span><span class="p">.</span> <span class="n" style="color: #333;">Look</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">README</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="mosel"><span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">mtCDNAape</span><span class="p">/</span> <span class="n" style="color: #333;">folder</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bounds</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">w</span> <span class="p">(</span><span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span><span class="p">)</span> <span class="n" style="color: #333;">ratios</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="mosel"><span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">classes</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">tp</span> <span class="p">(</span><span class="m" style="color: #099;">0.0001</span><span class="p">,</span> <span class="m" style="color: #099;">0.5</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">w0</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">(</span><span class="m" style="color: #099;">0.5</span><span class="p">,</span> <span class="m" style="color: #099;">1.5</span><span class="p">)</span> <span class="n" style="color: #333;">for</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="mosel"><span class="n" style="color: #333;">w1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">d</span><span class="p">,</span><span class="n" style="color: #333;">e</span><span class="p">,</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">for</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="mosel"><span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">motivation</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bounds</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">site</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="mosel"><span class="n" style="color: #333;">class</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">represents</span> <span class="n" style="color: #333;">strong</span> <span class="n" style="color: #333;">purifying</span> <span class="n" style="color: #333;">selection</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">small</span> <span class="n" style="color: #333;">w0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="mosel"><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">class</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">should</span> <span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">sites</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">weak</span> <span class="n" style="color: #333;">purifying</span> <span class="n" style="color: #333;">selection</span> <span class="k" style="font-weight: 600;">with</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="mosel"><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">larger</span> <span class="n" style="color: #333;">w1</span><span class="p">.</span> <span class="n" style="color: #333;">However</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bounds</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">arbitrary</span><span class="p">.</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">datasets</span><span class="p">,</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="mosel"><span class="n" style="color: #333;">MLEs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">found</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bounds</span><span class="p">,</span> <span class="n" style="color: #333;">making</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">interpretation</span> <span class="n" style="color: #333;">awkward</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bounds</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span><span class="p">:</span> </span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="mosel"><span class="n" style="color: #333;">w0b</span><span class="p">[]={</span><span class="m" style="color: #099;">0.0001</span><span class="p">,</span> <span class="m" style="color: #099;">1.0</span><span class="p">},</span> <span class="n" style="color: #333;">w1b</span><span class="p">[]={</span><span class="m" style="color: #099;">0.01</span><span class="p">,</span> <span class="m" style="color: #099;">1.5</span><span class="p">}.</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">swap</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">estimates</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">w0</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">w0</span> <span class="p">></span> <span class="n" style="color: #333;">w1</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2018</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">:</span> <span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">Dirichlet</span> <span class="n" style="color: #333;">versus</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">priors</span> <span class="n" style="color: #333;">for</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="mosel"><span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">loci</span><span class="p">.</span> <span class="n" style="color: #333;">Since</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span> <span class="n" style="color: #333;">are</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="mosel"><span class="n" style="color: #333;">inconsistent</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">priors</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">value</span> <span class="p">(</span><span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">means</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="mosel"><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">prior</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">checked</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span> <span class="k" style="font-weight: 600;">to</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="mosel"><span class="n" style="color: #333;">make</span> <span class="n" style="color: #333;">sure</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">consistent</span><span class="p">:</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="mosel"></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="mosel"><span class="n" style="color: #333;">prior</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">Dirichlet</span> <span class="p">(</span><span class="n" style="color: #333;">dos</span> <span class="n" style="color: #333;">Reis</span> <span class="m" style="color: #099;">2014</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span><span class="p">.</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="mosel"><span class="n" style="color: #333;">prior</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">prior</span> <span class="p">(</span><span class="n" style="color: #333;">Zhu</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="m" style="color: #099;">2015</span><span class="p">).</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="mosel"></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">believe</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">similar</span> <span class="n" style="color: #333;">especially</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">loci</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">partitions</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">large</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">serious</span> <span class="n" style="color: #333;">comparisons</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">two</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="mosel"><span class="n" style="color: #333;">priors</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">published</span><span class="p">.</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="mosel"></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Adnan</span> <span class="n" style="color: #333;">Moussalli</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">pointing</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">errors</span><span class="p">.</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="mosel"></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">discovered</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mechanistic</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="mosel"><span class="n" style="color: #333;">substitution</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">implemented</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Yang</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">1998</span><span class="p">;</span> <span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">table</span> <span class="m" style="color: #099;">3</span><span class="p">),</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">seqtype</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">long</span> <span class="n" style="color: #333;">time</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="mosel"><span class="n" style="color: #333;">since</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.0</span> <span class="p">(</span><span class="m" style="color: #099;">2000</span><span class="p">)</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span><span class="p">.</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">2.0</span> <span class="p">(</span><span class="m" style="color: #099;">1999</span><span class="p">)</span> <span class="n" style="color: #333;">seems</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="mosel"><span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">soon</span> <span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">was</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="mosel"><span class="n" style="color: #333;">published</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">this</span><span class="p">.</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="mosel"></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">starts</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Markov</span> <span class="n" style="color: #333;">chain</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="mosel"><span class="n" style="color: #333;">codons</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">aggregate</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">states</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">merge</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">synonymous</span> <span class="n" style="color: #333;">codons</span></span>
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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="mosel"><span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">state</span> <span class="p">(</span><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">coded</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">approximate</span></span>
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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="mosel"><span class="n" style="color: #333;">formulation</span> <span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">process</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">state</span> <span class="n" style="color: #333;">aggregation</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">Markovian</span></span>
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74
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="mosel"><span class="n" style="color: #333;">anymore</span><span class="p">.</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">another</span> <span class="n" style="color: #333;">codon</span><span class="p">-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">substitution</span> <span class="k" style="font-weight: 600;">model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
77
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="mosel"><span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">treats</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acids</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ambiguities</span> <span class="n" style="color: #333;">codons</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">specified</span></span>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="mosel"><span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">seqtype</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">5.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">formulation</span><span class="p">.</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="mosel"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">categories</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">M2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">M8</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">unintentionally</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">10.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">changed</span></span>
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<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="mosel"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">back</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">10.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">details</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Yang</span> <span class="n" style="color: #333;">et</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="mosel"><span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="m" style="color: #099;">2005</span> <span class="n" style="color: #333;">MBE</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="mosel"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="mosel"></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2017</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="mosel"></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">caused</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">site</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">M8</span></span>
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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">NSsites</span> <span class="p">=</span> <span class="m" style="color: #099;">8</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">incorrect</span><span class="p">,</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">printing</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">warming</span></span>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="mosel"><span class="n" style="color: #333;">messages</span> <span class="n" style="color: #333;">like</span> <span class="s2" style="color: #d14;">"strange: f[ 5] = -0.0587063 very small."</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span></span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="mosel"><span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span><span class="p">-</span><span class="n" style="color: #333;">f</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">different</span></span>
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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="mosel"><span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.9f</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="nb" style="color: #0086b3;">log</span> <span class="n" style="color: #333;">likelihood</span></span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="mosel"><span class="k" style="font-weight: 600;">function</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">site</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">M8</span> <span class="p">(</span><span class="n" style="color: #333;">NSsites</span> <span class="p">=</span> <span class="m" style="color: #099;">8</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">calculated</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="mosel"><span class="n" style="color: #333;">incorrectly</span><span class="p">.</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="mosel"></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="mosel"></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="mosel"></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9f</span><span class="p">,</span> <span class="n" style="color: #333;">October</span> <span class="m" style="color: #099;">2017</span></span>
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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">baseml</span><span class="p">,</span> <span class="n" style="color: #333;">nonhomogeneous</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">nhomo</span> <span class="p">&</span> <span class="n" style="color: #333;">fix_kappa</span><span class="p">).</span> <span class="n" style="color: #333;">Those</span> <span class="n" style="color: #333;">models</span></span>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="mosel"><span class="n" style="color: #333;">allow</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">branches</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">Q</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="mosel"><span class="n" style="color: #333;">Roughly</span> <span class="n" style="color: #333;">nhomo</span> <span class="n" style="color: #333;">controls</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">base</span> <span class="n" style="color: #333;">frequency</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">gix_kappa</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="mosel"><span class="n" style="color: #333;">controls</span> <span class="n" style="color: #333;">kappa</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">exchangeability</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">b</span> <span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">d</span> <span class="n" style="color: #333;">e</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="mosel"><span class="n" style="color: #333;">GTR</span><span class="p">/</span><span class="n" style="color: #333;">REV</span><span class="p">,</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">example</span><span class="p">).</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="p">(</span><span class="n" style="color: #333;">nhomo</span> <span class="p">=</span> <span class="m" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">fix_kappa</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="mosel"><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">lets</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">define</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">types</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">branches</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="mosel"><span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">type</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">exchangeability</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">b</span> <span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">d</span> <span class="n" style="color: #333;">e</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">GTR</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">base</span> <span class="n" style="color: #333;">composition</span> <span class="k" style="font-weight: 600;">parameters</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">branches</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">types</span></span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">different</span> <span class="k" style="font-weight: 600;">parameters</span><span class="p">.</span> <span class="n" style="color: #333;">Branch</span> <span class="n" style="color: #333;">types</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">labeled</span> <span class="p">(</span><span class="n" style="color: #333;">using</span> <span class="p">#</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">$),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="mosel"><span class="m" style="color: #099;">0</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="p">....</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">labels</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">consecutive</span> <span class="n" style="color: #333;">positive</span> <span class="n" style="color: #333;">integers</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">old</span> <span class="k" style="font-weight: 600;">options</span> <span class="n" style="color: #333;">nhomo</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">GTR</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="k" style="font-weight: 600;">not</span></span>
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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="mosel"><span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">base</span> <span class="n" style="color: #333;">composition</span> <span class="k" style="font-weight: 600;">parameters</span><span class="p">.</span> <span class="k" style="font-weight: 600;">In</span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="mosel"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">update</span><span class="p">,</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">think</span> <span class="n" style="color: #333;">those</span> <span class="k" style="font-weight: 600;">options</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">work</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">models</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">edited</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span> <span class="p">(</span><span class="n" style="color: #333;">look</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">nhomo</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">baseml</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">baseml</span> <span class="p">&</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">i</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">fix_blength</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span></span>
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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">proportional</span><span class="p">),</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">proporational</span></span>
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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">given</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">proportionality</span> <span class="n" style="color: #333;">factor</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="mosel"><span class="n" style="color: #333;">estimated</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">ML</span><span class="p">.</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="mosel"></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">correctly</span> <span class="n" style="color: #333;">for</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">M0</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">fix_kappa</span> <span class="p">=</span> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">c</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">c</span><span class="p">-</span><span class="n" style="color: #333;">e</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">seqtype</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">).</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">analyzing</span> <span class="n" style="color: #333;">multiple</span></span>
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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="mosel"><span class="n" style="color: #333;">protein</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="p">(</span><span class="n" style="color: #333;">ndata</span> <span class="p">></span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">empirical</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">wag</span><span class="p">,</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="mosel"><span class="n" style="color: #333;">jtt</span><span class="p">,</span> <span class="n" style="color: #333;">dayhoff</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">all</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="mosel"><span class="n" style="color: #333;">later</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">analyzed</span> <span class="n" style="color: #333;">incorrectly</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">corresponding</span> <span class="p">+</span><span class="n" style="color: #333;">F</span></span>
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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="mosel"><span class="n" style="color: #333;">models</span><span class="p">,</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">is</span><span class="p">,</span> <span class="n" style="color: #333;">wag</span><span class="p">+</span><span class="n" style="color: #333;">F</span><span class="p">,</span> <span class="n" style="color: #333;">jtt</span><span class="p">+</span><span class="n" style="color: #333;">F</span><span class="p">,</span> <span class="n" style="color: #333;">dayhoff</span><span class="p">+</span><span class="n" style="color: #333;">F</span><span class="p">,</span> <span class="n" style="color: #333;">etc</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="mosel"><span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">later</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">equilibrium</span> <span class="n" style="color: #333;">amino</span></span>
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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="mosel"><span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">frequencies</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">taken</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">real</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">correctly</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="mosel"><span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">empirical</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span></span>
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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="mosel"><span class="n" style="color: #333;">recorded</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">update</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">April</span> <span class="m" style="color: #099;">2005</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">somehow</span></span>
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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="mosel"><span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">fixed</span><span class="p">,</span> <span class="n" style="color: #333;">even</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">version</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Nick</span></span>
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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="mosel"><span class="n" style="color: #333;">Goldman</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">again</span><span class="p">.</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="mosel"></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">evolver</span> <span class="p">(</span><span class="k" style="font-weight: 600;">options</span> <span class="m" style="color: #099;">5</span><span class="p">,</span> <span class="m" style="color: #099;">6</span><span class="p">,</span> <span class="m" style="color: #099;">7</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">simulating</span> <span class="n" style="color: #333;">nucleotide</span><span class="p">,</span> <span class="n" style="color: #333;">codon</span> <span class="k" style="font-weight: 600;">and</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="mosel"><span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">alignments</span><span class="p">).</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">choose</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">printing</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="mosel"><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">pattern</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequences</span> <span class="p">(</span><span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="mosel"><span class="n" style="color: #333;">beginning</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">MCbase</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">),</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="mosel"><span class="n" style="color: #333;">simulating</span> <span class="n" style="color: #333;">two</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">crashes</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">finishing</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="mosel"></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">crashes</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">mixture</span> <span class="k" style="font-weight: 600;">of</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="mosel"><span class="n" style="color: #333;">morphological</span> <span class="n" style="color: #333;">loci</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">molecular</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">morphological</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="mosel"><span class="n" style="color: #333;">loci</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">molecular</span> <span class="n" style="color: #333;">loci</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">this</span><span class="p">.</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">think</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">never</span> <span class="n" style="color: #333;">described</span> <span class="n" style="color: #333;">anyway</span><span class="p">.</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="mosel"></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="mosel"></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="mosel"></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2017</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">Edited</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">readme</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">license</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">GPL</span><span class="p">.</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="mosel"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="mosel"><span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">to</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">information</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="mosel"><span class="n" style="color: #333;">incorrectly</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">joint</span> <span class="p">(</span><span class="n" style="color: #333;">minimum</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">maximum</span><span class="p">)</span> <span class="n" style="color: #333;">bounds</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">using</span></span>
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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">symbol</span> <span class="s1" style="color: #d14;">'<'</span> <span class="k" style="font-weight: 600;">and</span> <span class="s1" style="color: #d14;">'>'</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">notation</span> <span class="s2" style="color: #d14;">"B()"</span><span class="p">,</span> <span class="s2" style="color: #d14;">"L()"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="mosel"><span class="s1" style="color: #d14;">'U()'</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">information</span> <span class="n" style="color: #333;">is</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">correctly</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="mosel"><span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">exists</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">Versions</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">earlier</span></span>
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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="mosel"><span class="n" style="color: #333;">were</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="mosel"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="mosel"></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="mosel"></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2017</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
169
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">Changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">loci</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="mosel"><span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">Dirichlet</span> <span class="p">(</span><span class="n" style="color: #333;">dos</span> <span class="n" style="color: #333;">Reis</span> <span class="m" style="color: #099;">2014</span><span class="p">),</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">updated</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span> <span class="k" style="font-weight: 600;">as</span></span>
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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="mosel"><span class="n" style="color: #333;">well</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">prior</span> <span class="p">(</span><span class="n" style="color: #333;">Zhu</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="m" style="color: #099;">2015</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">Bayes</span> <span class="n" style="color: #333;">factor</span> <span class="n" style="color: #333;">calculation</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">called</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="mosel"><span class="n" style="color: #333;">BFdriver</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">release</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">pdf</span> <span class="n" style="color: #333;">document</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="mosel"><span class="n" style="color: #333;">folder</span> <span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">DatingSoftBound</span><span class="p">/</span><span class="n" style="color: #333;">BFdriverDOC</span><span class="p">.</span><span class="n" style="color: #333;">pdf</span><span class="p">.</span> <span class="n" style="color: #333;">We</span> <span class="n" style="color: #333;">suggest</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">you</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="mosel"><span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">the</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="mosel"><span class="n" style="color: #333;">normal</span> <span class="n" style="color: #333;">approximation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">unreliable</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">power</span> <span class="n" style="color: #333;">posterior</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">close</span> <span class="k" style="font-weight: 600;">to</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">prior</span> <span class="p">(</span><span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">beta</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">small</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="mosel"></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">September</span> <span class="m" style="color: #099;">2016</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">GPL</span> <span class="n" style="color: #333;">license</span> <span class="n" style="color: #333;">statement</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">various</span> <span class="n" style="color: #333;">places</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">two</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">trees</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
187
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">model</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="mosel"><span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">correctly</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">later</span></span>
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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
189
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="mosel"><span class="n" style="color: #333;">trees</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">overcounts</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">lnL</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
190
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="mosel"><span class="n" style="color: #333;">parameter</span> <span class="n" style="color: #333;">estimates</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">printed</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
191
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="mosel"><span class="n" style="color: #333;">extra</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">more</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">less</span> <span class="nb" style="color: #0086b3;">random</span> <span class="n" style="color: #333;">numbers</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">vary</span> <span class="n" style="color: #333;">among</span></span>
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<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
192
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="mosel"><span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">runs</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">analysis</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="mosel"><span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.7</span><span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">versions</span> <span class="n" style="color: #333;">since</span> <span class="k" style="font-weight: 600;">then</span> <span class="k" style="font-weight: 600;">until</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="mosel"><span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Casey</span> <span class="n" style="color: #333;">Bergman</span><span class="p">.</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="mosel"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="mosel"></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="mosel"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2016</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span><span class="p">.</span> <span class="n" style="color: #333;">I</span></span>
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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="mosel"><span class="n" style="color: #333;">deleted</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">having</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">classes</span> <span class="n" style="color: #333;">under</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span></span>
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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="mosel"><span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">clade</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">C</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">assume</span> <span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">classes</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="mosel"><span class="n" style="color: #333;">difference</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">C</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">C</span><span class="p">,</span> <span class="n" style="color: #333;">w1</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="n" style="color: #333;">w1</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">free</span> <span class="n" style="color: #333;">parameter</span><span class="p">,</span> <span class="n" style="color: #333;">just</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">w0</span><span class="p">.</span> <span class="n" style="color: #333;">Both</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">ML</span> <span class="n" style="color: #333;">iteration</span> <span class="k" style="font-weight: 600;">and</span></span>
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205
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">C</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">allow</span> <span class="n" style="color: #333;">two</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">clades</span></span>
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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
206
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">types</span><span class="p">),</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">increase</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">clades</span> <span class="n" style="color: #333;">by</span> <span class="m" style="color: #099;">1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
207
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="mosel"><span class="n" style="color: #333;">roughly</span> <span class="n" style="color: #333;">increases</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">computation</span> <span class="n" style="color: #333;">by</span> <span class="m" style="color: #099;">10</span> <span class="n" style="color: #333;">times</span><span class="p">.</span> <span class="n" style="color: #333;">Also</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span></span>
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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
208
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="mosel"><span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">under</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">about</span> <span class="m" style="color: #099;">10</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">expensive</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">that</span></span>
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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
209
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="mosel"><span class="n" style="color: #333;">under</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">C</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">updated</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">section</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="mosel"><span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">old</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">M1</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">M2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="p">(</span><span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">M1a</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">M2a</span><span class="p">).</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="mosel"></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span> <span class="p">&</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">labels</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">symbol</span> <span class="p">#,</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">crash</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">caused</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">routine</span> <span class="n" style="color: #333;">for</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="mosel"><span class="n" style="color: #333;">reading</span> <span class="n" style="color: #333;">trees</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="mosel"></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">September</span> <span class="m" style="color: #099;">2015</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">seqtype</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">sequences</span><span class="p">)</span> <span class="n" style="color: #333;">crashes</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">dataset</span></span>
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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">large</span><span class="p">,</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">2</span><span class="n" style="color: #333;">M</span> <span class="n" style="color: #333;">sites</span><span class="p">,</span> <span class="n" style="color: #333;">say</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">due</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">stupid</span> <span class="n" style="color: #333;">bug</span></span>
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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">irrelevant</span> <span class="n" style="color: #333;">part</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">code</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">4.9</span><span class="n" style="color: #333;">a</span><span class="p">.</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="mosel"></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="mosel"></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.9</span><span class="p">,</span> <span class="n" style="color: #333;">January</span> <span class="m" style="color: #099;">2015</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">There</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">priors</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">locus</span> <span class="n" style="color: #333;">rates</span> <span class="p">(</span><span class="n" style="color: #333;">mu_i</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">rates</span></span>
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<td class="diff-line-num old old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">loci</span><span class="p">),</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">summarized</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Zhu</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">2014</span> <span class="n" style="color: #333;">Sys</span> <span class="n" style="color: #333;">Biol</span><span class="p">).</span> <span class="n" style="color: #333;">They</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">follows</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="mosel"> <span class="n" style="color: #333;">rgene_gamma</span> <span class="p">=</span> <span class="n" style="color: #333;">alpha_u</span> <span class="n" style="color: #333;">beta_u</span> <span class="n" style="color: #333;">alpha</span> <span class="n" style="color: #333;">prior</span> <span class="p">*</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">overall</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">genes</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="mosel"><span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">prior</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">prior</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">prior</span> <span class="p">=</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="mosel"><span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">dirichlet</span> <span class="n" style="color: #333;">prior</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="mosel"><span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">specifies</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">prior</span> <span class="k" style="font-weight: 600;">with</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="mosel"><span class="n" style="color: #333;">alpha_mu</span> <span class="p">=</span> <span class="m" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">beta_mu</span> <span class="p">=</span> <span class="m" style="color: #099;">1000</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">alpha</span> <span class="p">=</span> <span class="m" style="color: #099;">0.5</span><span class="p">.</span> <span class="n" style="color: #333;">Here</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">average</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="mosel"><span class="n" style="color: #333;">overall</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">0100</span><span class="p">/</span><span class="m" style="color: #099;">1000</span> <span class="p">=</span> <span class="m" style="color: #099;">.1</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">time</span> <span class="n" style="color: #333;">unit</span><span class="p">.</span> <span class="n" style="color: #333;">alpha</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="mosel"><span class="p">=</span> <span class="m" style="color: #099;">0.5</span> <span class="n" style="color: #333;">describes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">extent</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">variation</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">loci</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="mosel"> <span class="n" style="color: #333;">rgene_gamma</span> <span class="p">=</span> <span class="m" style="color: #099;">100</span> <span class="m" style="color: #099;">1000</span> <span class="m" style="color: #099;">0.5</span> <span class="m" style="color: #099;">0</span> <span class="p">*</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">locus</span> <span class="n" style="color: #333;">rates</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="mosel"> <span class="n" style="color: #333;">sigma2_gamma</span> <span class="p">=</span> <span class="m" style="color: #099;">4</span> <span class="m" style="color: #099;">100</span> <span class="m" style="color: #099;">0.5</span> <span class="p">*</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">sigma</span><span class="p">^</span><span class="m" style="color: #099;">2</span> <span class="p">(</span><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">clock</span><span class="p">=</span><span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">sigma2_i</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">has</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">alpha_u</span><span class="p">,</span> <span class="n" style="color: #333;">beta_u</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span><span class="p">,</span> <span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">format</span><span class="p">.</span> </span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">setting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">finetune</span> <span class="n" style="color: #333;">step</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="mosel"><span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">MCMC</span> <span class="n" style="color: #333;">algorithms</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">parameter</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="mosel"><span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">own</span> <span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">lengths</span><span class="p">.</span> <span class="k" style="font-weight: 600;">As</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num old old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="mosel"><span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">adjusted</span> <span class="n" style="color: #333;">during</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">burn</span><span class="p">-</span><span class="k" style="font-weight: 600;">in</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cannot</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">or</span></span>
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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">line</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
253
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="mosel"> <span class="n" style="color: #333;">finetune</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="m" style="color: #099;">.0040</span> <span class="m" style="color: #099;">0.030</span> <span class="m" style="color: #099;">0.015</span> <span class="m" style="color: #099;">0.03</span> <span class="m" style="color: #099;">.55</span> <span class="p">*</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="n" style="color: #333;">rates</span><span class="p">,</span> <span class="n" style="color: #333;">mixing</span><span class="p">,</span> <span class="n" style="color: #333;">paras</span><span class="p">,</span> <span class="n" style="color: #333;">RateParas</span></span>
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<td class="diff-line-num old old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
254
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">is</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">ignored</span><span class="p">.</span> </span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">density</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">S2N</span> <span class="p">(</span><span class="n" style="color: #333;">skew</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">normals</span><span class="p">)</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="mosel"><span class="n" style="color: #333;">incorrectly</span> <span class="n" style="color: #333;">implemented</span><span class="p">.</span> <span class="k" style="font-weight: 600;">While</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">formula</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="mosel"> <span class="n" style="color: #333;">p0</span> <span class="p">*</span> <span class="n" style="color: #333;">f1</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">+</span> <span class="p">(</span><span class="m" style="color: #099;">1</span> <span class="p">-</span> <span class="n" style="color: #333;">p0</span><span class="p">)</span> <span class="n" style="color: #333;">f2</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">formula</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">is</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="mosel"> <span class="n" style="color: #333;">p0</span> <span class="p">*</span> <span class="n" style="color: #333;">f1</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">+</span> <span class="n" style="color: #333;">f2</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
261
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="mosel"><span class="n" style="color: #333;">Basically</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">skew</span><span class="p">-</span><span class="n" style="color: #333;">normal</span> <span class="n" style="color: #333;">densities</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">weights</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">make</span> <span class="n" style="color: #333;">sure</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">effective</span> <span class="n" style="color: #333;">prior</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
263
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">sensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">mistake</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">little</span> <span class="n" style="color: #333;">impact</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="mosel"><span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Mario</span> <span class="n" style="color: #333;">dos</span> <span class="n" style="color: #333;">Reis</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="mosel"></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="mosel"></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.8</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">August</span> <span class="m" style="color: #099;">2014</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">baseml</span> <span class="p">(</span><span class="n" style="color: #333;">nhomo</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">4</span><span class="p">).</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nonhomogeneous</span> <span class="n" style="color: #333;">GTR</span></span>
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<td class="diff-line-num old old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">REV</span><span class="p">)</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">abcde</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">branch</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
273
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="mosel"><span class="n" style="color: #333;">specifications</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">follows</span><span class="p">.</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span><span class="p">=</span><span class="m" style="color: #099;">7</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">fix_kappa</span><span class="p">=</span><span class="m" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">rate</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">abcde</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GTR</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">whole</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
276
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span><span class="p">=</span><span class="m" style="color: #099;">7</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">fix_kappa</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">rate</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">abcde</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GTR</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">branch</span><span class="p">.</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="mosel"><span class="k" style="font-weight: 600;">In</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.8</span><span class="p">,</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">second</span> <span class="n" style="color: #333;">option</span> <span class="p">(</span><span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">abcde</span> <span class="k" style="font-weight: 600;">parameters</span></span>
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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
279
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">whole</span> <span class="n" style="color: #333;">tree</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">implemented</span><span class="p">,</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">matter</span> <span class="n" style="color: #333;">whether</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">choose</span> <span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">or</span></span>
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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="mosel"><span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">fix_kappa</span><span class="p">.</span> <span class="n" style="color: #333;">After</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">change</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">use</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">fix_kappa</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nhomo</span></span>
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<td class="diff-line-num old old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
281
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="mosel"><span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">consistent</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">HKY</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">GTR</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">HKY</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">specifications</span></span>
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<td class="diff-line-num old old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">always</span> <span class="n" style="color: #333;">been</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">follows</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
284
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">fix_kappa</span><span class="p">=</span><span class="m" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">kappa</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">HKY</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">whole</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">fix_kappa</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">kappa</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">HKY</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">branch</span><span class="p">.</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="mosel"> </span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="mosel"><span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">frequency</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">every</span></span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span></span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">method</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">calculating</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">expected</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="mosel"><span class="n" style="color: #333;">changes</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">nucleotide</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">nucleotide</span> <span class="n" style="color: #333;">j</span> <span class="n" style="color: #333;">along</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">under</span></span>
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<td class="diff-line-num old old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nonhomogeneous</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">4</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">called</span> <span class="n" style="color: #333;">EMC</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="mosel"><span class="n" style="color: #333;">accounts</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">fact</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">base</span> <span class="n" style="color: #333;">frequencies</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">changing</span> <span class="n" style="color: #333;">over</span></span>
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<td class="diff-line-num old old_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="mosel"><span class="n" style="color: #333;">time</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">does</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rate</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">substitution</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">invoked</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">using</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="mosel"><span class="n" style="color: #333;">RateAncestor</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">verbose</span> <span class="p">=</span> <span class="m" style="color: #099;">1.</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">carefully</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">options</span> <span class="n" style="color: #333;">nhomo</span><span class="p">=</span><span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">and</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="mosel"><span class="m" style="color: #099;">5</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">well</span> <span class="n" style="color: #333;">tested</span><span class="p">.</span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="mosel"></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="mosel"></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="mosel"></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.8</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2014</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="mosel"></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">loci</span> <span class="p">(</span><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ndata</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">more</span><span class="p">)</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="mosel"><span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">changed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">Dirichlet</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span><span class="p">.</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">old</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">replaced</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">unavailable</span> <span class="n" style="color: #333;">anymore</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">new</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="mosel"><span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">Dirichlet</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">decribed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">paper</span> </span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="mosel"><span class="n" style="color: #333;">dos</span> <span class="n" style="color: #333;">Reis</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">.,</span> <span class="n" style="color: #333;">T</span><span class="p">.</span> <span class="n" style="color: #333;">Zhu</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Z</span><span class="p">.</span> <span class="n" style="color: #333;">Yang</span><span class="p">.</span> <span class="m" style="color: #099;">2014.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">impact</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">prior</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="mosel"><span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">Bayesian</span> <span class="n" style="color: #333;">estimation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">divergence</span> <span class="n" style="color: #333;">times</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">multiple</span></span>
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<td class="diff-line-num old old_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="mosel"><span class="n" style="color: #333;">loci</span><span class="p">.</span> <span class="n" style="color: #333;">Syst</span><span class="p">.</span> <span class="n" style="color: #333;">Biol</span><span class="p">.</span> <span class="m" style="color: #099;">63</span><span class="p">:</span><span class="m" style="color: #099;">555</span><span class="p">-</span><span class="m" style="color: #099;">565.</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Bayesian</span> <span class="n" style="color: #333;">method</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">estimating</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">t</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span></span>
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<td class="diff-line-num old old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="mosel"><span class="n" style="color: #333;">ratio</span> <span class="n" style="color: #333;">w</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">comparisons</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">is</span> </span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="mosel"> <span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="p">-</span><span class="m" style="color: #099;">3</span> <span class="p">*</span> <span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">:</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">Bayesian</span></span>
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<td class="diff-line-num old old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
316
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="mosel"> <span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="p">-</span><span class="m" style="color: #099;">3</span> <span class="m" style="color: #099;">1.1</span> <span class="m" style="color: #099;">1.1</span> <span class="m" style="color: #099;">1.1</span> <span class="m" style="color: #099;">2.2</span> <span class="p">*</span> <span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">:</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">Bayesian</span></span>
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<td class="diff-line-num old old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">four</span> <span class="n" style="color: #333;">numbers</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">priors</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">t</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span> <span class="p">(</span><span class="n" style="color: #333;">a_t</span> <span class="n" style="color: #333;">b_t</span> <span class="n" style="color: #333;">a_w</span> <span class="n" style="color: #333;">b_w</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">method</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">described</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">paper</span><span class="p">:</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="mosel"><span class="n" style="color: #333;">Angelis</span><span class="p">,</span> <span class="n" style="color: #333;">K</span><span class="p">.,</span> <span class="n" style="color: #333;">M</span><span class="p">.</span> <span class="n" style="color: #333;">dos</span> <span class="n" style="color: #333;">Reis</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Z</span><span class="p">.</span> <span class="n" style="color: #333;">Yang</span><span class="p">.</span> <span class="m" style="color: #099;">2014.</span> <span class="n" style="color: #333;">Bayesian</span> <span class="n" style="color: #333;">estimation</span> <span class="k" style="font-weight: 600;">of</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="mosel"><span class="n" style="color: #333;">nonsynonymous</span><span class="p">/</span><span class="n" style="color: #333;">synonymous</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">sequence</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="mosel"><span class="n" style="color: #333;">comparisons</span><span class="p">.</span> <span class="n" style="color: #333;">Mol</span><span class="p">.</span> <span class="n" style="color: #333;">Biol</span><span class="p">.</span> <span class="n" style="color: #333;">Evol</span><span class="p">.</span> <span class="m" style="color: #099;">31</span><span class="p">:</span><span class="m" style="color: #099;">1902</span><span class="p">-</span><span class="m" style="color: #099;">1913.</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="mosel"></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">baseml</span><span class="p">,</span> <span class="n" style="color: #333;">codeml</span><span class="p">,</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">).</span> <span class="k" style="font-weight: 600;">In</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.7</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">disabled</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">reading</span> <span class="n" style="color: #333;">species</span> <span class="n" style="color: #333;">indexes</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">example</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="mosel"><span class="m" style="color: #099;">19</span><span class="p">,</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">mean</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="m" style="color: #099;">19</span><span class="n" style="color: #333;">th</span> <span class="n" style="color: #333;">sequence</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">alignment</span><span class="p">).</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">back</span><span class="p">.</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.7</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">problem</span><span class="p">.</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="mosel"></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">paml</span> <span class="m" style="color: #099;">4.6</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.7</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">have</span> <span class="nf" style="color: #900; font-weight: 600;">stop</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="mosel"><span class="n" style="color: #333;">codons</span><span class="p">.</span> <span class="nf" style="color: #900; font-weight: 600;">Stop</span> <span class="n" style="color: #333;">codons</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">always</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">disallowed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">models</span></span>
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<td class="diff-line-num old old_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="mosel"><span class="n" style="color: #333;">implemented</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.6</span><span class="p">-</span><span class="m" style="color: #099;">4.7</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="nf" style="color: #900; font-weight: 600;">stop</span> <span class="n" style="color: #333;">codon</span></span>
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<td class="diff-line-num old old_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codons</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">site</span> <span class="p">(</span><span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">in</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="mosel"><span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">into</span> <span class="p">???</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">processed</span></span>
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<td class="diff-line-num old old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">usual</span> <span class="n" style="color: #333;">way</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">should</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="mosel"><span class="n" style="color: #333;">likelihood</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">column</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">removed</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="mosel"><span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">idea</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">incorrect</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">gives</span> <span class="n" style="color: #333;">wrong</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">if</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">do</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">ambiguity</span> <span class="n" style="color: #333;">characters</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="mosel"><span class="n" style="color: #333;">choose</span> <span class="n" style="color: #333;">cleandata</span> <span class="p">=</span> <span class="m" style="color: #099;">0.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">this</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">idea</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">really</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="mosel"><span class="n" style="color: #333;">useful</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">good</span> <span class="n" style="color: #333;">advice</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">of</span> <span class="nf" style="color: #900; font-weight: 600;">stop</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="mosel"><span class="n" style="color: #333;">codons</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">analyzed</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span></span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="mosel"> </span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.7</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">October</span> <span class="m" style="color: #099;">2013</span></span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="mosel"></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">mutation</span><span class="p">-</span><span class="n" style="color: #333;">selection</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Nielsen</span> <span class="p">(</span><span class="m" style="color: #099;">2008</span><span class="p">)</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">noted</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">site</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">branch</span><span class="p">-</span><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">but</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="mosel"></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">modified</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">infinitesites</span> <span class="n" style="color: #333;">program</span><span class="p">,</span> <span class="n" style="color: #333;">which</span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="mosel"><span class="n" style="color: #333;">generates</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">limiting</span> <span class="n" style="color: #333;">distribution</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">amount</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">data</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="mosel"><span class="n" style="color: #333;">approaches</span> <span class="n" style="color: #333;">infinity</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">works</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">clock</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span></span>
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353
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="mosel"><span class="n" style="color: #333;">relaxed</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span><span class="p">=</span><span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">3</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">mcmctree</span> <span class="n" style="color: #333;">tutorial</span> <span class="n" style="color: #333;">explains</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="mosel"><span class="n" style="color: #333;">how</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">program</span><span class="p">.</span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.7</span><span class="p">,</span> <span class="n" style="color: #333;">January</span> <span class="m" style="color: #099;">2013</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="mosel"></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">version</span> <span class="n" style="color: #333;">includes</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">method</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">dating</span> <span class="n" style="color: #333;">divergences</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="mosel"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">sampled</span> <span class="n" style="color: #333;">tips</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">viral</span> <span class="n" style="color: #333;">datasets</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">node</span> <span class="n" style="color: #333;">ages</span> <span class="k" style="font-weight: 600;">in</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span> <span class="n" style="color: #333;">rooted</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">generated</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">a</span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="mosel"><span class="n" style="color: #333;">birth</span><span class="p">-</span><span class="n" style="color: #333;">death</span><span class="p">-</span><span class="n" style="color: #333;">sequential</span><span class="p">-</span><span class="n" style="color: #333;">sampling</span> <span class="k" style="font-weight: 600;">model</span><span class="p">,</span> <span class="n" style="color: #333;">described</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Stadler</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">2012</span> <span class="n" style="color: #333;">Syst</span> <span class="n" style="color: #333;">Biol</span><span class="p">,</span> <span class="n" style="color: #333;">submitted</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">SIV</span><span class="p">/</span><span class="n" style="color: #333;">HIV</span><span class="p">-</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">dataset</span> <span class="n" style="color: #333;">analyzed</span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">paper</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">TipDate</span><span class="p">/</span> <span class="n" style="color: #333;">folder</span><span class="p">.</span> <span class="n" style="color: #333;">Look</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">readme</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="mosel"><span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">there</span><span class="p">.</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="mosel"></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.6</span> <span class="n" style="color: #333;">crashes</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">lot</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">ambiguity</span> <span class="n" style="color: #333;">codons</span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">precisely</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">total</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">fully</span> <span class="n" style="color: #333;">determined</span></span>
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<td class="diff-line-num old old_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="mosel"><span class="n" style="color: #333;">codons</span> <span class="p">(</span><span class="m" style="color: #099;">61</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">standard</span> <span class="n" style="color: #333;">code</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">ambiguous</span> <span class="n" style="color: #333;">codons</span> <span class="n" style="color: #333;">exceed</span> <span class="m" style="color: #099;">127.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">using</span> <span class="s2" style="color: #d14;">"unsigned char"</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">represent</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codons</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">go</span> <span class="k" style="font-weight: 600;">from</span> <span class="m" style="color: #099;">0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
371
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">255</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">represent</span> <span class="m" style="color: #099;">256</span> <span class="n" style="color: #333;">distinct</span> <span class="n" style="color: #333;">codons</span><span class="p">.</span> <span class="n" style="color: #333;">Somehow</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">this</span></span>
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<td class="diff-line-num old old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="s2" style="color: #d14;">"char"</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">systems</span> <span class="n" style="color: #333;">goes</span> <span class="k" style="font-weight: 600;">from</span> <span class="p">-</span><span class="m" style="color: #099;">128</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">127.</span> <span class="n" style="color: #333;">Can</span><span class="s1" style="color: #d14;">'t</span></span>
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<td class="diff-line-num old old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="mosel"><span class="s1" style="color: #d14;">remember why I made the change. Anyway this is now fixed. Versions</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="mosel"><span class="s1" style="color: #d14;">4.5 or earlier do not have this problem. Thanks to David Yu for</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="mosel"><span class="s1" style="color: #d14;">pointing out the problem.</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 4.6, September 2012</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="mosel"><span class="s1" style="color: #d14;">(*) baseml. The model of autocorrelated-rates among sites (Yang 1995</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="mosel"><span class="s1" style="color: #d14;">Genetics 139:993-1005) is broken in paml versions 4.3 to 4.5</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="mosel"><span class="s1" style="color: #d14;">inclusive. Earlier versions were apparently fine. When you select</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="mosel"><span class="s1" style="color: #d14;">the auto-discrete-gamma model (alpha > 0, rho > 0) or the</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="mosel"><span class="s1" style="color: #d14;">nonparametric autocorrelated-rates model (fix_alpha = 0, ncatG = 3,</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="mosel"><span class="s1" style="color: #d14;">nparK = 4), the program aborts with the following error message:</span></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="mosel"><span class="s1" style="color: #d14;">"Error: use 10, 20, 32, 64, 128, 512, 1024 for npoints for legendre.."</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="mosel"><span class="s1" style="color: #d14;">This is now fixed. The option of nparK = 3 seems to have problems in</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="mosel"><span class="s1" style="color: #d14;">all versions, and the program prints out the following warning</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="mosel"><span class="s1" style="color: #d14;">message. </span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="mosel"><span class="s1" style="color: #d14;">"nparK==3, double stochastic, may not work. Use nparK=4?"</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="mosel"><span class="s1" style="color: #d14;">This option is supposed to fit a Markov-dependent model with equal</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="mosel"><span class="s1" style="color: #d14;">proportions in the rate categies. I have not got time to investigate</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="mosel"><span class="s1" style="color: #d14;">this option, but a glance at table 3 in that paper indicates that this</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="mosel"><span class="s1" style="color: #d14;">model was not used in the table and probably never properly</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="mosel"><span class="s1" style="color: #d14;">implemented, so please follow the advice and use nparK = 4 instead.</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="mosel"><span class="s1" style="color: #d14;">(*) codeml. I have now added the site model M2a_rel of Weadick & Chang</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="mosel"><span class="s1" style="color: #d14;">(2012 Mol. Biol. Evol.), in which w2 > 0. This is specified using</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="mosel"><span class="s1" style="color: #d14;">NSsites = 22 while model M2a is specified as NSsites = 2 (with w2 ></span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="mosel"><span class="s1" style="color: #d14;">1). M2a_rel is the null model for the likelihood ratio test based on</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="mosel"><span class="s1" style="color: #d14;">clade model C, suggested by Weadick & Chang (2012 Mol. Biol. Evol.).</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="mosel"><span class="s1" style="color: #d14;">Note that the very old site model M2 from Nielsen & Yang (1998</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="mosel"><span class="s1" style="color: #d14;">Genetics) assumes w0 = 0. Yang, Wong, Nielsen (2005 MBE) changed the</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="mosel"><span class="s1" style="color: #d14;">model so that 0 < w0 < 1 and renamed the model M2a. My tests using</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="mosel"><span class="s1" style="color: #d14;">the versions around that time reveals the following:</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="mosel"><span class="s1" style="color: #d14;">3.13d (M2): w0 = 0, w2 > 0</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="mosel"><span class="s1" style="color: #d14;">3.14a (M2a): w0 > 0, w2 >= 1</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="mosel"><span class="s1" style="color: #d14;">3.14b (M2a): w0 > 0, w2 >= 1</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="mosel"><span class="s1" style="color: #d14;">If seems that when we changed M2 into M2a, we also changed the</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="mosel"><span class="s1" style="color: #d14;">constraint on w2. I don'</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">copy</span> <span class="k" style="font-weight: 600;">of</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.14</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">check</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">basseml</span> <span class="p">&</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">option</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="mosel"> <span class="n" style="color: #333;">bootstrap</span> <span class="p">=</span> <span class="m" style="color: #099;">1000</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="mosel"><span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">produce</span> <span class="m" style="color: #099;">1000</span> <span class="n" style="color: #333;">bootstrap</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">boot</span><span class="p">.</span><span class="n" style="color: #333;">txt</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span></span>
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423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="mosel"><span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.4</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.5</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">garbiage</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">created</span></span>
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424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="mosel"><span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">bootstrap</span> <span class="n" style="color: #333;">datasets</span><span class="p">.</span> <span class="n" style="color: #333;">Versions</span> <span class="m" style="color: #099;">4.3</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">were</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span></span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="mosel"></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">evolver</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">simulation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">sequences</span> <span class="p">(</span><span class="n" style="color: #333;">evolver</span> <span class="m" style="color: #099;">6</span></span>
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<td class="diff-line-num old old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="mosel"><span class="n" style="color: #333;">MCcodon</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">genetic</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">different</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="mosel"><span class="n" style="color: #333;">universal</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">conceptual</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">made</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">has</span></span>
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<td class="diff-line-num old old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
430
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="mosel"><span class="n" style="color: #333;">been</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">previous</span> <span class="n" style="color: #333;">versions</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">simulation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="mosel"><span class="n" style="color: #333;">allowed</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">assumed</span> <span class="n" style="color: #333;">incorrectly</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">setting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">frequencies</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="mosel"><span class="nf" style="color: #900; font-weight: 600;">stop</span> <span class="n" style="color: #333;">codons</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">sufficient</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">results</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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433
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="mosel"><span class="n" style="color: #333;">zero</span> <span class="n" style="color: #333;">frequencies</span> <span class="n" style="color: #333;">allow</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">identify</span> <span class="n" style="color: #333;">the</span> <span class="nf" style="color: #900; font-weight: 600;">stop</span> <span class="n" style="color: #333;">codons</span></span>
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<td class="diff-line-num old old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
434
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="mosel"><span class="n" style="color: #333;">correctly</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">needs</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">table</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">know</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">changes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">synonymous</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">nonsynonymous</span><span class="p">.</span> <span class="n" style="color: #333;">evolver</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span></span>
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436
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="mosel"><span class="n" style="color: #333;">universal</span> <span class="n" style="color: #333;">code</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">simulate</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">sequences</span><span class="p">.</span> <span class="n" style="color: #333;">Simulation</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
437
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="mosel"><span class="n" style="color: #333;">universal</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">simulation</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="mosel"><span class="n" style="color: #333;">mitochondrial</span> <span class="n" style="color: #333;">code</span> <span class="p">(</span><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">example</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">affcted</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="mosel"><span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">although</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">impact</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">slight</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="mosel"><span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">added</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">MCcodon</span><span class="p">.</span><span class="n" style="color: #333;">dat</span> <span class="n" style="color: #333;">right</span> <span class="n" style="color: #333;">below</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="mosel"><span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">frequencies</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">tells</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">genetic</span> <span class="n" style="color: #333;">code</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="mosel"><span class="m" style="color: #099;">1</span> <span class="p">*</span> <span class="n" style="color: #333;">genetic</span> <span class="n" style="color: #333;">code</span> <span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">universal</span><span class="p">;</span> <span class="m" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">mammalian</span> <span class="n" style="color: #333;">mt</span><span class="p">;</span> <span class="m" style="color: #099;">2</span><span class="p">-</span><span class="m" style="color: #099;">10</span><span class="p">:</span><span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">below</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">checks</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="nf" style="color: #900; font-weight: 600;">stop</span> <span class="n" style="color: #333;">codons</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">frequency</span> <span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">that</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">frequencies</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sense</span> <span class="n" style="color: #333;">codons</span> <span class="k" style="font-weight: 600;">sum</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Mario</span> <span class="n" style="color: #333;">dos</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="mosel"><span class="n" style="color: #333;">Reis</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">pointing</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">out</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="mosel"><span class="p">(*)</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">found</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">calculation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">rates</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="mosel"><span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">correlated</span><span class="p">-</span><span class="n" style="color: #333;">rates</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span><span class="p">=</span><span class="m" style="color: #099;">3</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="k" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="mosel"><span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4</span> <span class="p">(</span><span class="n" style="color: #333;">July</span> <span class="m" style="color: #099;">2007</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.5</span> <span class="p">(</span><span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2011</span><span class="p">),</span> <span class="n" style="color: #333;">inclusive</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="mosel"><span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">calculated</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">multiplying</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">conditional</span> <span class="n" style="color: #333;">densities</span> <span class="k" style="font-weight: 600;">of</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="mosel"><span class="n" style="color: #333;">equation</span> <span class="p">(</span><span class="m" style="color: #099;">7</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Rannala</span> <span class="p">&</span> <span class="n" style="color: #333;">Yand</span> <span class="p">(</span><span class="m" style="color: #099;">2007</span><span class="p">)</span> <span class="n" style="color: #333;">over</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">interior</span> <span class="n" style="color: #333;">nodes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="mosel"><span class="n" style="color: #333;">master</span> <span class="n" style="color: #333;">tree</span> <span class="p">(</span><span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">Figure</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">paper</span><span class="p">).</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rA</span> <span class="n" style="color: #333;">used</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">current</span> <span class="n" style="color: #333;">branch</span><span class="p">:</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">instead</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span></span>
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456
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="mosel"><span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">branch</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">formula</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">root</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">master</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">interior</span> <span class="n" style="color: #333;">nodes</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="mosel"><span class="n" style="color: #333;">impact</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">posterior</span> <span class="n" style="color: #333;">time</span> <span class="n" style="color: #333;">estimates</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">expected</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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459
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="mosel"><span class="n" style="color: #333;">small</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">seriously</span> <span class="n" style="color: #333;">violated</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">over</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="mosel"><span class="n" style="color: #333;">neighboring</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">concern</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.5</span><span class="p">,</span> <span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2011</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span></span>
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467
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="mosel"><span class="n" style="color: #333;">nonhomogeneous</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">nhomo</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">4</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">works</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="mosel"><span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">sites</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">rates</span></span>
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469
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">partition</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">Also</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">joint</span></span>
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470
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="mosel"><span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">only</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">marginal</span> <span class="n" style="color: #333;">reconstruction</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">prints</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">called</span> <span class="n" style="color: #333;">FigTree</span><span class="p">.</span><span class="n" style="color: #333;">tre</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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473
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="mosel"><span class="n" style="color: #333;">current</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">directory</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">readable</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">FigTree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">branch</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="mosel"><span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">show</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">posterior</span> <span class="n" style="color: #333;">means</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">times</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bars</span> <span class="n" style="color: #333;">generated</span> <span class="n" style="color: #333;">by</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="mosel"><span class="n" style="color: #333;">FigTree</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">indicate</span> <span class="n" style="color: #333;">the</span> <span class="m" style="color: #099;">95</span><span class="p">%</span> <span class="n" style="color: #333;">CIs</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">to</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="mosel"><span class="n" style="color: #333;">deal</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">TipDate</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">viral</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dates</span><span class="p">.</span> <span class="n" style="color: #333;">See</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="mosel"><span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">TipDate</span><span class="p">/</span><span class="n" style="color: #333;">README</span><span class="p">.</span><span class="n" style="color: #333;">txt</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">notes</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">May</span> <span class="m" style="color: #099;">2011</span></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">adjusting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">step</span></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="mosel"><span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">proposals</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">MCMC</span> <span class="n" style="color: #333;">algorithm</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="mosel"><span class="n" style="color: #333;">burn</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">adjust</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">values</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">initial</span> <span class="n" style="color: #333;">values</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="mosel"></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">iteration</span> <span class="n" style="color: #333;">method</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">updates</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">length</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">time</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">method</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">free</span><span class="p">-</span><span class="n" style="color: #333;">ratios</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span></span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="mosel"><span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.3</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">d</span> <span class="n" style="color: #333;">inclusive</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">see</span></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="mosel"><span class="n" style="color: #333;">messages</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">screen</span><span class="p">:</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="mosel"><span class="n" style="color: #333;">Warning</span> <span class="n" style="color: #333;">rounding</span> <span class="n" style="color: #333;">error</span><span class="p">?</span> <span class="n" style="color: #333;">b</span><span class="p">=</span><span class="m" style="color: #099;">3</span> <span class="n" style="color: #333;">cycle</span><span class="p">=</span><span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">lnL</span><span class="p">=</span><span class="m" style="color: #099;">6036.9413757</span> <span class="c1" style="color: #998; font-style: italic;">!= 6070.1069284 </span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.2</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> </span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Tae</span><span class="p">-</span><span class="n" style="color: #333;">Kun</span> <span class="n" style="color: #333;">Seo</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="mosel"></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="mosel"></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2011</span></span>
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<td class="diff-line-num old old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="mosel"><span class="n" style="color: #333;">yn00</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">weighting</span> <span class="p">(</span><span class="n" style="color: #333;">weighting</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="mosel"><span class="n" style="color: #333;">calculation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">dN</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">dS</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">YN00</span> <span class="n" style="color: #333;">method</span> <span class="p">(</span><span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Nielsen</span> <span class="m" style="color: #099;">2000</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="mosel"><span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">since</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span> <span class="p">(</span><span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2010</span><span class="p">).</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span></span>
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<td class="diff-line-num old old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="mosel"><span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">character</span> <span class="n" style="color: #333;">coding</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="mosel"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">Versions</span> <span class="m" style="color: #099;">4.4</span><span class="p">,</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">c</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span></span>
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<td class="diff-line-num old old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="mosel"><span class="n" style="color: #333;">typically</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">crash</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">result</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">weighting</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span></span>
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<td class="diff-line-num old old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="mosel"><span class="n" style="color: #333;">affected</span><span class="p">.</span> <span class="n" style="color: #333;">Versions</span> <span class="n" style="color: #333;">before</span> <span class="m" style="color: #099;">4.4</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Charlie</span></span>
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<td class="diff-line-num old old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">ucl</span><span class="p">.</span><span class="n" style="color: #333;">ac</span><span class="p">.</span><span class="n" style="color: #333;">uk</span><span class="p">/</span><span class="n" style="color: #333;">discussions</span><span class="p">/</span><span class="n" style="color: #333;">viewtopic</span><span class="p">.</span><span class="n" style="color: #333;">php</span><span class="p">?</span><span class="n" style="color: #333;">t</span><span class="p">=</span><span class="m" style="color: #099;">8726</span><span class="p">&</span><span class="n" style="color: #333;">highlight</span><span class="p">=</span><span class="n" style="color: #333;">yn00</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="mosel"></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="mosel"></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="mosel"></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">August</span> <span class="m" style="color: #099;">2010</span></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="mosel"></span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">exotic</span> <span class="n" style="color: #333;">calibrations</span> <span class="p">(</span><span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">skew</span> <span class="n" style="color: #333;">normal</span></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">skew</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">sometimes</span> <span class="n" style="color: #333;">ignored</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">loci</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">partitions</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">species</span><span class="p">/</span><span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">loci</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">calibrations</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">bounds</span> <span class="p">(</span><span class="n" style="color: #333;">minimum</span><span class="p">,</span> <span class="n" style="color: #333;">maximum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">joint</span><span class="p">),</span> <span class="k" style="font-weight: 600;">or</span> <span class="k" style="font-weight: 600;">if</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">partitions</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">species</span><span class="p">/</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">the</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="mosel"><span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.1</span><span class="p">-</span><span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">b</span><span class="p">.</span> <span class="n" style="color: #333;">This</span></span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Mike</span> <span class="n" style="color: #333;">Steiper</span><span class="p">.</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="mosel"></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="mosel"></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="mosel"></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">July</span> <span class="m" style="color: #099;">2010</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">serious</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">discovered</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span></span>
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527
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">calculation</span> <span class="p">(</span><span class="n" style="color: #333;">usedata</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">).</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="mosel"><span class="n" style="color: #333;">child</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">root</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">locus</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">tip</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">MLEs</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">in</span><span class="p">.</span><span class="n" style="color: #333;">BV</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">assigned</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">wrong</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">so</span></span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="mosel"><span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">entirely</span> <span class="n" style="color: #333;">incorrect</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">different</span> <span class="k" style="font-weight: 600;">from</span></span>
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531
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="mosel"><span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">obtained</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">exact</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">calculation</span> <span class="p">(</span><span class="n" style="color: #333;">usedata</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">).</span></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="mosel"><span class="n" style="color: #333;">Suppose</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">locus</span> <span class="n" style="color: #333;">is</span> <span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">B</span><span class="p">),</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bifurcation</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span></span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="mosel"><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">A</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">B</span> <span class="n" style="color: #333;">representing</span> <span class="n" style="color: #333;">species</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">clades</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">tip</span><span class="p">,</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">incorrect</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">internal</span> <span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span></span>
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<td class="diff-line-num old old_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.2</span><span class="n" style="color: #333;">b</span> <span class="p">-</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">a</span><span class="p">.</span> <span class="n" style="color: #333;">Hopefully</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">is</span></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="mosel"><span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">corrected</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Mario</span> <span class="n" style="color: #333;">dos</span> <span class="n" style="color: #333;">Reis</span><span class="p">.</span></span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="mosel"></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">specification</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">B</span> <span class="n" style="color: #333;">bounds</span> <span class="k" style="font-weight: 600;">to</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="mosel"><span class="n" style="color: #333;">allow</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tail</span> <span class="n" style="color: #333;">probabilities</span> <span class="p">(</span><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="mosel"><span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">at</span> <span class="m" style="color: #099;">2.5</span><span class="p">%)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">calibration</span><span class="p">.</span> <span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">table</span> <span class="m" style="color: #099;">8</span> <span class="k" style="font-weight: 600;">in</span></span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="mosel"><span class="n" style="color: #333;">pamlDOC</span><span class="p">.</span><span class="n" style="color: #333;">pdf</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">details</span><span class="p">.</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span></span>
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<td class="diff-line-num old old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="mosel"><span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">effective</span> <span class="n" style="color: #333;">prior</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">June</span> <span class="m" style="color: #099;">2010</span></span>
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547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">RateAncestor</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="p">).</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">codon</span></span>
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549
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="mosel"><span class="n" style="color: #333;">models</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">prints</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">translated</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acids</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">it</span></span>
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550
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="mosel"><span class="n" style="color: #333;">prints</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codons</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">caused</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">translation</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">incorrect</span><span class="p">,</span></span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="mosel"><span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">prints</span> <span class="n" style="color: #333;">something</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">h</span> <span class="k" style="font-weight: 600;">or</span></span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="mosel"><span class="n" style="color: #333;">H</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="p">,</span> <span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2010</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">I</span></span>
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<td class="diff-line-num old old_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="mosel"><span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">way</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">characters</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">coded</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">now</span><span class="p">.</span></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="mosel"></span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">3</span> <span class="n" style="color: #333;">Mgene</span> <span class="n" style="color: #333;">option</span><span class="p">).</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">assign</span> <span class="n" style="color: #333;">different</span></span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="mosel"><span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">genes</span> <span class="p">(</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">parations</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">assumes</span></span>
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557
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="mosel"><span class="n" style="color: #333;">global</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">clock</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">fails</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">print</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="mosel"><span class="n" style="color: #333;">relative</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">seems</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">between</span></span>
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<td class="diff-line-num old old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="mosel"><span class="m" style="color: #099;">3.13</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.14</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">since</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="nb" style="color: #0086b3;">log</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">estimates</span></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="mosel"><span class="k" style="font-weight: 600;">of</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">problem</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">MLEs</span> <span class="k" style="font-weight: 600;">of</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="mosel"><span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">genes</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">printed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">properly</span><span class="p">.</span></span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="mosel"></span>
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563
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="mosel"></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="mosel"></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">April</span> <span class="m" style="color: #099;">2010</span></span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="mosel"></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="mosel"><span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.2</span><span class="p">,</span> <span class="m" style="color: #099;">4.3</span><span class="p">,</span> <span class="m" style="color: #099;">4.4</span><span class="p">,</span> <span class="n" style="color: #333;">Clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">print</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">w</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="mosel"><span class="n" style="color: #333;">estimates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">classes</span> <span class="n" style="color: #333;">correctly</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">example</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="k" style="font-weight: 600;">in</span></span>
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569
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="mosel"><span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">datasets2</span><span class="p">/,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">looks</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span></span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="mosel"><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">class</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">1</span> <span class="m" style="color: #099;">2</span></span>
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572
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="mosel"><span class="n" style="color: #333;">proportion</span> <span class="m" style="color: #099;">0.48590</span> <span class="m" style="color: #099;">0.10718</span> <span class="m" style="color: #099;">0.40692</span></span>
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<td class="diff-line-num old old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
573
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">type</span> <span class="m" style="color: #099;">0</span><span class="p">:</span> <span class="m" style="color: #099;">0.10557</span> <span class="m" style="color: #099;">4.17186</span> <span class="m" style="color: #099;">4.17186</span></span>
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<td class="diff-line-num old old_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
574
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">type</span> <span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="m" style="color: #099;">0.10557</span> <span class="m" style="color: #099;">4.17186</span> <span class="m" style="color: #099;">3.05340</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="mosel"></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="mosel"><span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">results</span> <span class="p">(</span><span class="k" style="font-weight: 600;">from</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.1</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> </span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="mosel"></span>
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578
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="mosel"><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">class</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">1</span> <span class="m" style="color: #099;">2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
579
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="mosel"><span class="n" style="color: #333;">proportion</span> <span class="m" style="color: #099;">0.48590</span> <span class="m" style="color: #099;">0.10718</span> <span class="m" style="color: #099;">0.40692</span></span>
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<td class="diff-line-num old old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
580
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="mosel"><span class="n" style="color: #333;">background</span> <span class="n" style="color: #333;">w</span> <span class="m" style="color: #099;">0.10557</span> <span class="m" style="color: #099;">4.17186</span> <span class="m" style="color: #099;">3.05340</span></span>
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<td class="diff-line-num old old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
581
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="mosel"><span class="n" style="color: #333;">foreground</span> <span class="n" style="color: #333;">w</span> <span class="m" style="color: #099;">0.10557</span> <span class="m" style="color: #099;">4.17186</span> <span class="m" style="color: #099;">0.95081</span></span>
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<td class="diff-line-num old old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
582
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
583
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">w2</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w3</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">class</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">incorrectly</span> <span class="n" style="color: #333;">printed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">w2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
584
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="mosel"><span class="n" style="color: #333;">equal</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">w1</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">lnL</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">etc</span><span class="p">.</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.2</span><span class="p">,</span> <span class="m" style="color: #099;">4.3</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.4</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.1</span> <span class="k" style="font-weight: 600;">and</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="mosel"><span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">versions</span> <span class="n" style="color: #333;">appear</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">Also</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">clade</span></span>
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<td class="diff-line-num old old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">C</span> <span class="n" style="color: #333;">appears</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">fine</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">now</span><span class="p">.</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">cajawe</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span> <span class="p">(</span><span class="n" style="color: #333;">see</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="mosel"><span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">ucl</span><span class="p">.</span><span class="n" style="color: #333;">ac</span><span class="p">.</span><span class="n" style="color: #333;">uk</span><span class="p">/</span><span class="n" style="color: #333;">discussions</span><span class="p">/</span><span class="n" style="color: #333;">viewtopic</span><span class="p">.</span><span class="n" style="color: #333;">php</span><span class="p">?</span><span class="n" style="color: #333;">p</span><span class="p">=</span><span class="m" style="color: #099;">28240</span><span class="p">#</span><span class="m" style="color: #099;">28240</span><span class="p">).</span></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="mosel"></span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="mosel"></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="mosel"></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.4</span><span class="p">,</span> <span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2010</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="mosel"></span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">way</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">characters</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">coded</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">programs</span><span class="p">,</span> <span class="n" style="color: #333;">which</span></span>
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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="mosel"><span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">essentially</span> <span class="n" style="color: #333;">every</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">modified</span><span class="p">.</span> <span class="n" style="color: #333;">It</span></span>
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597
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">likely</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">bugs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">during</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">process</span><span class="p">.</span> </span>
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598
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
599
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">iteration</span> <span class="n" style="color: #333;">algorithm</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">method</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">applied</span></span>
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600
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">sites</span> <span class="p">(</span><span class="n" style="color: #333;">seqtype</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span> <span class="p">></span></span>
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<td class="diff-line-num old old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
601
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="mosel"><span class="m" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">method</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">broken</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.2</span><span class="p">-</span><span class="m" style="color: #099;">4.3</span><span class="n" style="color: #333;">b</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
602
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="mosel"><span class="n" style="color: #333;">iteration</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">fail</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">converge</span><span class="p">,</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">messages</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span></span>
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603
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="mosel"><span class="n" style="color: #333;">printed</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">monitor</span><span class="p">:</span> </span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="mosel"><span class="s2" style="color: #d14;">"Warning rounding error? b=5 cycle=0 lnL=1718.5667685 != 1749.4724545"</span><span class="p">.</span></span>
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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="mosel"></span>
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606
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">prior</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">alpha</span> <span class="p"><</span><span class="m" style="color: #099;">1</span><span class="p">/</span><span class="m" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">initial</span></span>
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607
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="mosel"><span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">generated</span> <span class="n" style="color: #333;">incorrectly</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="mosel"></span>
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609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="mosel"></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="mosel"></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.3</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">November</span> <span class="m" style="color: #099;">2009</span></span>
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612
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
613
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.2</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
614
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="mosel"><span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">ignore</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">minimum</span> <span class="n" style="color: #333;">age</span> <span class="n" style="color: #333;">constraint</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">root</span> <span class="n" style="color: #333;">age</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">uses</span></span>
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<td class="diff-line-num old old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
615
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">bound</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">RootAge</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">there</span></span>
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<td class="diff-line-num old old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">root</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">minimum</span><span class="p">-</span><span class="n" style="color: #333;">age</span> <span class="n" style="color: #333;">constraint</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span></span>
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<td class="diff-line-num old old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
617
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="mosel"><span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span></span>
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<td class="diff-line-num old old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="mosel"><span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">bound</span><span class="p">,</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">minimum</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">bound</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">distribution</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
619
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="mosel"><span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">problem</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">4.2</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">4.3</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
620
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="mosel"><span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.1</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Mathieu</span></span>
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<td class="diff-line-num old old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="mosel"><span class="n" style="color: #333;">Groussin</span><span class="p">.</span></span>
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622
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="mosel"></span>
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623
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="mosel"><span class="n" style="color: #333;">evolver</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">back</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">printing</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">site</span></span>
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624
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="mosel"><span class="n" style="color: #333;">pattern</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequences</span> <span class="p">(</span><span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">beginning</span> <span class="k" style="font-weight: 600;">of</span></span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">MCbase</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">).</span> <span class="n" style="color: #333;">Use</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">pattern</span> <span class="n" style="color: #333;">counts</span> <span class="n" style="color: #333;">takes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="mosel"><span class="n" style="color: #333;">less</span> <span class="n" style="color: #333;">disk</span> <span class="n" style="color: #333;">space</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">removed</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.2</span><span class="n" style="color: #333;">b</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
627
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="mosel"><span class="n" style="color: #333;">algorithm</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">collaspsing</span> <span class="n" style="color: #333;">sites</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">patterns</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">rewritten</span><span class="p">.</span></span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="mosel"></span>
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629
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="mosel"></span>
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630
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="mosel"></span>
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631
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.3</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">October</span> <span class="m" style="color: #099;">2009</span></span>
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632
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
633
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.3</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">root</span></span>
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<td class="diff-line-num old old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
634
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="mosel"><span class="n" style="color: #333;">age</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">proposed</span> <span class="n" style="color: #333;">incorrectly</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">effect</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">appears</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
635
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="mosel"><span class="n" style="color: #333;">subtle</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">hard</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">assess</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num old old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
636
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="mosel"><span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">incorrect</span><span class="p">.</span> <span class="n" style="color: #333;">Here</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bit</span> <span class="n" style="color: #333;">more</span></span>
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<td class="diff-line-num old old_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
637
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="mosel"><span class="n" style="color: #333;">detail</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">internal</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">node</span> <span class="n" style="color: #333;">age</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">too</span> <span class="n" style="color: #333;">high</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
638
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">caused</span> <span class="n" style="color: #333;">loss</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">significant</span> <span class="n" style="color: #333;">digits</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">smart</span> <span class="n" style="color: #333;">reflection</span> <span class="n" style="color: #333;">algorithm</span></span>
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<td class="diff-line-num old old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
639
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="mosel"><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">reflects</span> <span class="n" style="color: #333;">proposed</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">feasible</span> <span class="n" style="color: #333;">interval</span><span class="p">.</span> <span class="n" style="color: #333;">This</span></span>
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640
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="mosel"><span class="n" style="color: #333;">update</span> <span class="n" style="color: #333;">fixes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span> <span class="n" style="color: #333;">Please</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">version</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">reanalyze</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="mosel"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.3</span><span class="p">.</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.2</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">supplies</span> <span class="n" style="color: #333;">compiling</span> <span class="k" style="font-weight: 600;">options</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">hard</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="mosel"><span class="n" style="color: #333;">minimum</span> <span class="n" style="color: #333;">hard</span> <span class="n" style="color: #333;">maximum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hard</span> <span class="n" style="color: #333;">minimum</span> <span class="n" style="color: #333;">soft</span> <span class="n" style="color: #333;">maximum</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">executables</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">called</span> <span class="n" style="color: #333;">mcmctreeHH</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mcmctreeHS</span><span class="p">.</span> <span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">commands</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">compiling</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="mosel"><span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">beginning</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.3</span><span class="p">,</span> <span class="n" style="color: #333;">August</span> <span class="m" style="color: #099;">2009</span></span>
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651
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">approximate</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">unreliable</span><span class="p">,</span></span>
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653
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="mosel"><span class="n" style="color: #333;">because</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Hessian</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">calculated</span> <span class="n" style="color: #333;">reliably</span><span class="p">,</span> <span class="n" style="color: #333;">especially</span> <span class="k" style="font-weight: 600;">if</span></span>
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654
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">estimates</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">are</span> <span class="m" style="color: #099;">0.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span></span>
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655
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="mosel"><span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">approach</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Seo</span><span class="p">,</span> <span class="n" style="color: #333;">Kishino</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Thorne</span> <span class="p">(</span><span class="m" style="color: #099;">2004</span><span class="p">),</span> <span class="n" style="color: #333;">which</span></span>
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656
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="mosel"><span class="n" style="color: #333;">appears</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">stable</span><span class="p">.</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="mosel"></span>
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658
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span> <span class="p">&</span> <span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">programs</span> <span class="k" style="font-weight: 600;">to</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">fasta</span> <span class="n" style="color: #333;">alignments</span></span>
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659
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="mosel"><span class="n" style="color: #333;">directly</span><span class="p">,</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">length</span></span>
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660
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="mosel"><span class="n" style="color: #333;">automatically</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">multiple</span></span>
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661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="mosel"><span class="n" style="color: #333;">alignments</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">is</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ndata</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">higher</span><span class="p">.</span></span>
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662
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="mosel"></span>
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664
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="mosel"></span>
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665
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.2</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">April</span> <span class="m" style="color: #099;">2009</span></span>
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666
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="mosel"></span>
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667
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">There</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">leads</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">crash</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">usedata</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">when</span></span>
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668
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">loci</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">ambiguity</span> <span class="n" style="color: #333;">characters</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">loci</span> <span class="k" style="font-weight: 600;">do</span></span>
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669
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="mosel"><span class="k" style="font-weight: 600;">not</span><span class="p">.</span> <span class="n" style="color: #333;">usedata</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">invokes</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">codeml</span> <span class="k" style="font-weight: 600;">to</span></span>
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670
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="mosel"><span class="n" style="color: #333;">calculate</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">maximum</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">estimates</span> <span class="p">(</span><span class="n" style="color: #333;">MLEs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span></span>
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671
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variances</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">MLEs</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">temporary</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">alignment</span></span>
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672
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="mosel"><span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">loci</span> <span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">?.</span><span class="n" style="color: #333;">txt</span><span class="p">)</span> <span class="n" style="color: #333;">generated</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">mcmctree</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">garbiage</span> <span class="k" style="font-weight: 600;">and</span></span>
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673
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">unreadable</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">baseml</span> <span class="p">(</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">codeml</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">corrected</span><span class="p">.</span></span>
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674
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">replace</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">wrong</span> <span class="n" style="color: #333;">alignment</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">locus</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">your</span></span>
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675
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="mosel"><span class="n" style="color: #333;">original</span> <span class="n" style="color: #333;">alignment</span> <span class="k" style="font-weight: 600;">and</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">baseml</span> <span class="n" style="color: #333;">outside</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.)</span></span>
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676
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="mosel"></span>
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677
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="mosel"></span>
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678
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="mosel"><span class="n" style="color: #333;">All</span> <span class="n" style="color: #333;">programs</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">rewrote</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">collapsing</span> <span class="n" style="color: #333;">sites</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">patterns</span><span class="p">.</span></span>
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679
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">impact</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">evolver</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span></span>
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680
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="mosel"><span class="n" style="color: #333;">produce</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="s2" style="color: #d14;">"pattern-count"</span> <span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">anymore</span><span class="p">.</span> <span class="n" style="color: #333;">Now</span> <span class="n" style="color: #333;">two</span></span>
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681
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="mosel"><span class="n" style="color: #333;">formats</span> <span class="p">(</span><span class="n" style="color: #333;">paml</span><span class="p">/</span><span class="n" style="color: #333;">phylip</span> <span class="n" style="color: #333;">format</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">PAUP</span> <span class="n" style="color: #333;">nexus</span> <span class="n" style="color: #333;">format</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">used</span><span class="p">,</span> <span class="n" style="color: #333;">specified</span></span>
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<td class="diff-line-num old old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
682
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="mosel"><span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">file</span> <span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.,</span> <span class="n" style="color: #333;">MCbase</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
683
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="mosel"><span class="n" style="color: #333;">MCcodon</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span> <span class="n" style="color: #333;">MCaa</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">pattern</span><span class="p">-</span><span class="k" style="font-weight: 600;">count</span> <span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">accepted</span></span>
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684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="mosel"><span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">baseml</span><span class="p">,</span> <span class="n" style="color: #333;">codeml</span><span class="p">,</span> <span class="n" style="color: #333;">etc</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">section</span> <span class="n" style="color: #333;">on</span> <span class="s2" style="color: #d14;">"Site pattern</span></span>
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685
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="mosel"><span class="s2" style="color: #d14;">counts"</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span><span class="p">).</span></span>
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686
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="mosel"></span>
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687
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span> <span class="p">&</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
688
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">clock</span><span class="p">=</span><span class="m" style="color: #099;">6</span><span class="p">),</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">generates</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">message</span><span class="p">:</span></span>
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689
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="mosel"><span class="s2" style="color: #d14;">"need fossils for this locus"</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">example</span><span class="p">,</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
690
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="mosel"><span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="p">/</span><span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">MouseLemurs</span><span class="p">/</span><span class="n" style="color: #333;">codonml2</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span> <span class="n" style="color: #333;">will</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">so</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span></span>
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<td class="diff-line-num old old_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
691
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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692
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
693
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.2</span> <span class="n" style="color: #333;">concerning</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">free</span><span class="p">-</span><span class="n" style="color: #333;">ratios</span></span>
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<td class="diff-line-num old old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="mosel"><span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">Yang</span> <span class="m" style="color: #099;">1998</span> <span class="n" style="color: #333;">MBE</span><span class="p">)</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">properly</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.2</span><span class="n" style="color: #333;">a</span> <span class="p">(</span><span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">the</span></span>
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695
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="mosel"><span class="n" style="color: #333;">notes</span> <span class="n" style="color: #333;">for</span> <span class="m" style="color: #099;">4.2</span><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">below</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">are</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="mosel"><span class="n" style="color: #333;">exactly</span> <span class="m" style="color: #099;">7</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">types</span> <span class="p">(</span><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">you</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">free</span><span class="p">-</span><span class="n" style="color: #333;">ratios</span> <span class="k" style="font-weight: 600;">model</span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="mosel"><span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="m" style="color: #099;">5</span><span class="p">-</span><span class="n" style="color: #333;">species</span> <span class="n" style="color: #333;">tree</span><span class="p">)</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">numbers</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">branch</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="mosel"><span class="n" style="color: #333;">types</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">hope</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">finally</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="mosel"></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="mosel"></span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="mosel"></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.2</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2009</span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="mosel"></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="mosel"></span>
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705
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">Two</span> <span class="n" style="color: #333;">bugs</span> <span class="n" style="color: #333;">were</span> <span class="n" style="color: #333;">known</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.2</span></span>
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706
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="mosel"><span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">rewrote</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span><span class="p">-</span><span class="n" style="color: #333;">site</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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707
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="mosel"><span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">null</span> <span class="n" style="color: #333;">hypothesis</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span><span class="p">-</span><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">test</span> <span class="p">(</span><span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span></span>
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708
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="mosel"><span class="n" style="color: #333;">NSsites</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">fix_omega</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">omega</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
709
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">Yang</span><span class="p">,</span> <span class="n" style="color: #333;">Wong</span> <span class="p">&</span> <span class="n" style="color: #333;">Nielsen</span> <span class="p">(</span><span class="m" style="color: #099;">2005</span><span class="p">),</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Zhang</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">2005</span><span class="p">).</span> <span class="n" style="color: #333;">The</span></span>
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710
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="mosel"><span class="n" style="color: #333;">alternative</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">fix_omega</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fine</span><span class="p">.</span></span>
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711
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
712
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">second</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">free</span><span class="p">-</span><span class="n" style="color: #333;">ratios</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">Yang</span> <span class="m" style="color: #099;">1998</span> <span class="n" style="color: #333;">MBE</span><span class="p">).</span></span>
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713
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="mosel"></span>
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714
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">incorrect</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">ignored</span></span>
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715
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="mosel"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4.2</span><span class="p">.</span> <span class="n" style="color: #333;">Both</span> <span class="n" style="color: #333;">mistakes</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">update</span><span class="p">.</span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">W</span><span class="p">.</span><span class="n" style="color: #333;">P</span><span class="p">.</span> <span class="n" style="color: #333;">Zhou</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">BYLee</span><span class="p">.</span></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="mosel"></span>
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719
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="mosel"></span>
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720
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
721
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4.2</span><span class="p">,</span> <span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2008</span></span>
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722
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
723
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="mosel"><span class="n" style="color: #333;">MCMCtree</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">lower</span> <span class="n" style="color: #333;">bound</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">upper</span> <span class="n" style="color: #333;">bound</span></span>
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724
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">changed</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">improper</span> <span class="n" style="color: #333;">density</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">equation</span> <span class="p">(</span><span class="m" style="color: #099;">15</span><span class="p">)</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Rannala</span></span>
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725
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">2006</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">lower</span> <span class="n" style="color: #333;">bound</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">noted</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">push</span> <span class="n" style="color: #333;">up</span> <span class="n" style="color: #333;">divergence</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="n" style="color: #333;">a</span></span>
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726
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="mosel"><span class="n" style="color: #333;">feature</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">consider</span> <span class="n" style="color: #333;">undesirable</span><span class="p">.</span> <span class="n" style="color: #333;">Now</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">truncated</span> <span class="n" style="color: #333;">Cauchy</span> <span class="n" style="color: #333;">distribution</span></span>
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<td class="diff-line-num old old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
727
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">described</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">detail</span> <span class="n" style="color: #333;">somewhere</span><span class="p">.</span></span>
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728
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
729
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">MCMC</span> <span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span> <span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">change</span></span>
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<td class="diff-line-num old old_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
730
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="mosel"><span class="n" style="color: #333;">this</span><span class="p">,</span> <span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">mcmctree</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span><span class="p">:</span></span>
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731
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="mosel"> <span class="n" style="color: #333;">mcmcfile</span> <span class="p">=</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">out</span> </span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="mosel"></span>
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733
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">Clade</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">C</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">D</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">extended</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">accommodate</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">two</span></span>
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<td class="diff-line-num old old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">types</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">old</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">accept</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">types</span> <span class="n" style="color: #333;">only</span><span class="p">,</span> <span class="n" style="color: #333;">referred</span></span>
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<td class="diff-line-num old old_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
735
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">foreground</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">background</span> <span class="n" style="color: #333;">branches</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">structure</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">new</span></span>
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<td class="diff-line-num old old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
736
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="mosel"><span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">below</span><span class="p">.</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">branch</span><span class="p">/</span><span class="n" style="color: #333;">node</span> <span class="n" style="color: #333;">numbers</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span></span>
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<td class="diff-line-num old old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
737
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="mosel"><span class="n" style="color: #333;">types</span> <span class="p">(</span><span class="k" style="font-weight: 600;">with</span> <span class="p">#</span><span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">followed</span> <span class="n" style="color: #333;">by</span> <span class="p">#</span><span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="p">#</span><span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="p">#</span><span class="m" style="color: #099;">3</span><span class="p">,</span> <span class="p">...).</span> <span class="k" style="font-weight: 600;">As</span></span>
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<td class="diff-line-num old old_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
738
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="mosel"><span class="n" style="color: #333;">before</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">C</span> <span class="n" style="color: #333;">only</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
739
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">D</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">expensive</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="mosel"><span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">expect</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">C</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">work</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">branch</span></span>
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<td class="diff-line-num old old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
741
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="mosel"><span class="n" style="color: #333;">types</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">additional</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">BEB</span> <span class="n" style="color: #333;">computation</span> <span class="n" style="color: #333;">is</span> <span class="m" style="color: #099;">10</span></span>
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<td class="diff-line-num old old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
742
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="mosel"><span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">expensive</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
743
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
744
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="mosel"><span class="n" style="color: #333;">Site</span> <span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">Proportion</span> <span class="n" style="color: #333;">w</span> <span class="n" style="color: #333;">ratio</span></span>
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<td class="diff-line-num old old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
745
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
746
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="mosel"> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">p0</span> <span class="m" style="color: #099;">0</span> <span class="p"><</span> <span class="n" style="color: #333;">w0</span> <span class="p"><</span> <span class="m" style="color: #099;">1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
747
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="mosel"> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">p1</span> <span class="n" style="color: #333;">w1</span> <span class="p">(</span><span class="n" style="color: #333;">w1</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">C</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
748
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="mosel"> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">p2</span> <span class="n" style="color: #333;">w2</span><span class="p">,</span> <span class="n" style="color: #333;">w3</span><span class="p">,</span> <span class="n" style="color: #333;">w4</span><span class="p">,</span> <span class="p">...</span></span>
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749
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="mosel"></span>
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750
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">fixing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">w</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">C</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">follows</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">example</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">are</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="mosel"><span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">types</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="p">(</span><span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">table</span> <span class="n" style="color: #333;">above</span><span class="p">),</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">w</span> <span class="n" style="color: #333;">fixed</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="mosel"><span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">w4</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="mosel"> <span class="n" style="color: #333;">fix_omega</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span></span>
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756
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="mosel"> <span class="n" style="color: #333;">omega</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">clade</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">compared</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">whether</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">w</span> <span class="n" style="color: #333;">is</span> <span class="p">></span> <span class="m" style="color: #099;">1.</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">chemical</span> <span class="n" style="color: #333;">properties</span><span class="p">,</span> <span class="n" style="color: #333;">specified</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="mosel"><span class="n" style="color: #333;">using</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">aaDist</span> <span class="p">=</span> <span class="m" style="color: #099;">7.</span> <span class="n" style="color: #333;">Under</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">model</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">types</span> <span class="k" style="font-weight: 600;">of</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="mosel"><span class="n" style="color: #333;">branches</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">just</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">labelling</span></span>
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765
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="mosel"><span class="n" style="color: #333;">branches</span><span class="p">).</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">estimates</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">w</span><span class="s1" style="color: #d14;">'s,</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="mosel"><span class="s1" style="color: #d14;">depending on specifications in the file OmegaAA.dat. This model seems</span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="mosel"><span class="s1" style="color: #d14;">to be broken for a long time since its implementation. Look at the</span></span>
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768
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="mosel"><span class="s1" style="color: #d14;">readme.txt file in examples/mtCDNAape/.</span></span>
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769
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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770
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 4.1, August 2008</span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="mosel"><span class="s1" style="color: #d14;">MCMCtree: A few changes have been introduced to this program. The</span></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="mosel"><span class="s1" style="color: #d14;">format for specifying fossil calibrations in the tree file has been</span></span>
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776
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="mosel"><span class="s1" style="color: #d14;">changed, so that the gamma distribution is specified as '</span><span class="n" style="color: #333;">G</span><span class="p">(</span><span class="n" style="color: #333;">alpha</span><span class="p">,</span></span>
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777
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="mosel"><span class="n" style="color: #333;">beta</span><span class="p">)</span><span class="s1" style="color: #d14;">' and the old format '</span><span class="p">></span><span class="m" style="color: #099;">0.6</span><span class="p">=</span><span class="m" style="color: #099;">0.7</span><span class="p"><</span><span class="m" style="color: #099;">0.8</span><span class="s1" style="color: #d14;">' does not work anymore. The</span></span>
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778
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="mosel"><span class="s1" style="color: #d14;">bounds can be specified using either the old form '</span><span class="p"><</span><span class="m" style="color: #099;">0.8</span><span class="s1" style="color: #d14;">' or the new</span></span>
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779
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="mosel"><span class="s1" style="color: #d14;">form '</span><span class="n" style="color: #333;">U</span><span class="p">(</span><span class="m" style="color: #099;">0.8</span><span class="p">)</span><span class="s1" style="color: #d14;">'. Two exotic distributions, skew normal and skew t, are</span></span>
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780
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="mosel"><span class="s1" style="color: #d14;">added, using the format '</span><span class="n" style="color: #333;">SN</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">shape</span><span class="p">)</span><span class="s1" style="color: #d14;">' and '</span><span class="n" style="color: #333;">ST</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">,</span></span>
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781
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="mosel"><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">)</span><span class="s1" style="color: #d14;">'. I edited the documentation pamlDOC.pdf and</span></span>
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782
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="mosel"><span class="s1" style="color: #d14;">rewrote the part for mcmctree. The format of the MCMC output file</span></span>
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783
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="mosel"><span class="s1" style="color: #d14;">mcmc.out has been modified so that it is readable by Andrew Rambaut'</span><span class="n" style="color: #333;">s</span></span>
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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="mosel"><span class="n" style="color: #333;">Tracer</span> <span class="n" style="color: #333;">program</span><span class="p">.</span> <span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">MCMCtree</span> <span class="n" style="color: #333;">starts</span> <span class="n" style="color: #333;">taking</span> <span class="n" style="color: #333;">samples</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">writing</span></span>
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785
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="mosel"><span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">burnin</span><span class="p">.</span></span>
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786
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">mutation</span><span class="p">-</span><span class="n" style="color: #333;">selection</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Nielsen</span> <span class="p">(</span><span class="m" style="color: #099;">2008</span></span>
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788
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="mosel"><span class="n" style="color: #333;">Mol</span><span class="p">.</span> <span class="n" style="color: #333;">Biol</span><span class="p">.</span> <span class="n" style="color: #333;">Evol</span><span class="p">.</span> <span class="m" style="color: #099;">25</span><span class="p">,</span> <span class="m" style="color: #099;">568</span><span class="p">-</span><span class="m" style="color: #099;">579</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">options</span></span>
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789
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="mosel"></span>
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790
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="mosel"> <span class="n" style="color: #333;">CodonFreq</span> <span class="p">=</span> <span class="m" style="color: #099;">6</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">7</span> <span class="p">*</span> <span class="m" style="color: #099;">6</span><span class="p">:</span><span class="n" style="color: #333;">FMutSel0</span><span class="p">,</span> <span class="m" style="color: #099;">7</span><span class="p">:</span><span class="n" style="color: #333;">FMutSel</span></span>
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791
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="mosel"> <span class="n" style="color: #333;">estFreq</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span></span>
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792
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
793
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="mosel"><span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">mtCDNAape</span><span class="p">/</span><span class="n" style="color: #333;">codeml</span><span class="p">.</span><span class="n" style="color: #333;">HC</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">duplicate</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span> <span class="m" style="color: #099;">1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
794
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">paper</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">seems</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mlc</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">while</span></span>
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<td class="diff-line-num old old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
795
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="mosel"><span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rst</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rst1</span> <span class="n" style="color: #333;">files</span><span class="p">.</span></span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="mosel"></span>
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797
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
798
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">model</span><span class="p">):</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">analyzed</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
799
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">NSsites</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">main</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span></span>
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800
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="mosel"><span class="n" style="color: #333;">includes</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">line</span> <span class="s2" style="color: #d14;">"w ratios as labels for TreeView:"</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
801
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.15</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span></span>
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<td class="diff-line-num old old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
802
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">had</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">dN</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">intended</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
803
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="mosel"><span class="n" style="color: #333;">original</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="p">(</span><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">nucleotide</span></span>
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<td class="diff-line-num old old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
804
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="mosel"><span class="n" style="color: #333;">substitutions</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">codon</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">affect</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
805
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="mosel"><span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">model</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
806
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="mosel"><span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">now</span><span class="p">.</span></span>
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807
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
808
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">discrete</span><span class="p">-</span><span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span><span class="p">):</span> <span class="n" style="color: #333;">My</span> <span class="n" style="color: #333;">intention</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span></span>
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810
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mean</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">median</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">represent</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">rates</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">category</span></span>
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<td class="diff-line-num old old_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
811
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="mosel"><span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">discrete</span><span class="p">-</span><span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">implemented</span><span class="p">.</span> <span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">Yang</span> <span class="p">(</span><span class="m" style="color: #099;">1994</span></span>
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<td class="diff-line-num old old_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="mosel"><span class="n" style="color: #333;">J</span><span class="p">.</span> <span class="n" style="color: #333;">Mol</span><span class="p">.</span> <span class="n" style="color: #333;">Evol</span><span class="p">.</span> <span class="m" style="color: #099;">39</span><span class="p">:</span><span class="m" style="color: #099;">306</span><span class="p">-</span><span class="m" style="color: #099;">314</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">distinction</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">caused</span></span>
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<td class="diff-line-num old old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
813
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="mosel"><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">recent</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">median</span> <span class="n" style="color: #333;">instead</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">affects</span> <span class="n" style="color: #333;">baseml</span></span>
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<td class="diff-line-num old old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
814
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="mosel"><span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.15</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">earlier</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4</span></span>
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<td class="diff-line-num old old_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
815
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="mosel"><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">later</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">codeml</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">a</span> <span class="p">&</span> <span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">b</span> <span class="n" style="color: #333;">were</span> <span class="n" style="color: #333;">incorrect</span> <span class="k" style="font-weight: 600;">while</span></span>
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<td class="diff-line-num old old_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
816
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="mosel"><span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">versions</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">hope</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span></span>
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<td class="diff-line-num old old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">c</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
819
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
820
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span> <span class="n" style="color: #333;">labels</span><span class="p">):</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span></span>
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<td class="diff-line-num old old_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
821
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">programs</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">branch</span><span class="p">-</span><span class="n" style="color: #333;">site</span></span>
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<td class="diff-line-num old old_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
822
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="mosel"><span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">labels</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">identify</span> <span class="n" style="color: #333;">branches</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">nested</span> <span class="n" style="color: #333;">clade</span></span>
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<td class="diff-line-num old old_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
823
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="mosel"><span class="n" style="color: #333;">label</span> <span class="p">($)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">used</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">confused</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branches</span></span>
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<td class="diff-line-num old old_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
824
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">labeled</span> <span class="n" style="color: #333;">correctly</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">think</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">c</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
825
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="mosel"></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">January</span> <span class="m" style="color: #099;">2008</span></span>
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<td class="diff-line-num old old_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
829
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">Changed</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">MaxRootAge</span></span>
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<td class="diff-line-num old old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">RootAge</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">any</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">formats</span><span class="p">:</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
832
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="mosel"> <span class="n" style="color: #333;">RootAge</span> <span class="p">=</span> <span class="p"><</span><span class="m" style="color: #099;">1.0</span> <span class="p">*</span> <span class="n" style="color: #333;">constraint</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">root</span> <span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">root</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
833
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="mosel"> <span class="n" style="color: #333;">RootAge</span> <span class="p">=</span> <span class="s1" style="color: #d14;">'<1.0'</span> <span class="p">*</span> <span class="n" style="color: #333;">constraint</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">root</span> <span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">root</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
834
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="mosel"> <span class="n" style="color: #333;">RootAge</span> <span class="p">=</span> <span class="p"><</span><span class="m" style="color: #099;">1.0</span><span class="p">></span><span class="m" style="color: #099;">0.8</span> <span class="p">*</span> <span class="n" style="color: #333;">constraint</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">root</span> <span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">root</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
835
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="mosel"> <span class="n" style="color: #333;">RootAge</span> <span class="p">=</span> <span class="s1" style="color: #d14;">'<1.0>0.8'</span> <span class="p">*</span> <span class="n" style="color: #333;">constraint</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">root</span> <span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">root</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
837
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="mosel"><span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">text</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">make</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">comprehensible</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
838
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
839
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="mosel"><span class="n" style="color: #333;">evolver</span> <span class="p">(</span><span class="n" style="color: #333;">option</span> <span class="m" style="color: #099;">8</span><span class="p">).</span> <span class="n" style="color: #333;">option</span> <span class="m" style="color: #099;">8</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">calculating</span> <span class="n" style="color: #333;">bipartition</span> <span class="n" style="color: #333;">distances</span></span>
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<td class="diff-line-num old old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
840
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="mosel"><span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">trees</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">broken</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">prepare</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
841
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="mosel"><span class="n" style="color: #333;">figure</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">forgot</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">afterwards</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span></span>
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<td class="diff-line-num old old_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
842
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="mosel"><span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
843
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
844
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
845
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">July</span> <span class="m" style="color: #099;">2007</span></span>
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846
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="mosel"><span class="n" style="color: #333;">mcmctree</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">MCMC</span> <span class="n" style="color: #333;">algorithm</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Rannala</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span> <span class="p">(</span><span class="m" style="color: #099;">2007</span><span class="p">)</span> <span class="n" style="color: #333;">dealing</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num old old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="mosel"><span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">drift</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">added</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">section</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">manual</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">mcmctree</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span></span>
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<td class="diff-line-num old old_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="mosel"><span class="n" style="color: #333;">rewritten</span><span class="p">.</span> <span class="n" style="color: #333;">An</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">set</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="mosel"><span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">DatingSoftBound</span><span class="p">/</span> <span class="n" style="color: #333;">folder</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
852
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="mosel"><span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">implements</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mutation</span><span class="p">-</span><span class="n" style="color: #333;">selection</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">codon</span></span>
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<td class="diff-line-num old old_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
853
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="mosel"><span class="n" style="color: #333;">substitution</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Nielsen</span> <span class="p">(</span><span class="m" style="color: #099;">2008</span><span class="p">).</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">should</span> <span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">more</span></span>
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854
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="mosel"><span class="n" style="color: #333;">details</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">better</span> <span class="n" style="color: #333;">tested</span><span class="p">,</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">example</span><span class="p">,</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="mosel"><span class="n" style="color: #333;">paper</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">written</span><span class="p">.</span></span>
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856
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
857
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="mosel"><span class="n" style="color: #333;">baseml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="nb" style="color: #0086b3;">log</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">rates</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">is</span><span class="p">,</span> <span class="n" style="color: #333;">when</span></span>
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<td class="diff-line-num old old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
858
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="mosel"><span class="n" style="color: #333;">alpha</span> <span class="p">></span> <span class="m" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">calculated</span> <span class="n" style="color: #333;">correctly</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="k" style="font-weight: 600;">not</span> <span class="k" style="font-weight: 600;">as</span></span>
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<td class="diff-line-num old old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
859
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="mosel"><span class="n" style="color: #333;">intended</span><span class="p">.</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.15</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
860
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="mosel"><span class="n" style="color: #333;">incorrect</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">am</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sure</span> <span class="n" style="color: #333;">about</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">kept</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
861
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="mosel"><span class="n" style="color: #333;">copy</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">median</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">represent</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">rates</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
862
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="mosel"><span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">category</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">discre</span><span class="p">-</span><span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">whereas</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">mean</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">intended</span><span class="p">.</span></span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="mosel"><span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">discussion</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">equation</span> <span class="p">(</span><span class="m" style="color: #099;">10</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">paragraph</span> <span class="n" style="color: #333;">below</span> <span class="n" style="color: #333;">it</span> <span class="k" style="font-weight: 600;">in</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="mosel"><span class="n" style="color: #333;">Yang</span> <span class="p">(</span><span class="m" style="color: #099;">1994.</span> <span class="n" style="color: #333;">J</span><span class="p">.</span> <span class="n" style="color: #333;">Mol</span><span class="p">.</span> <span class="n" style="color: #333;">Evol</span><span class="p">.</span> <span class="m" style="color: #099;">39</span><span class="p">:</span><span class="m" style="color: #099;">306</span><span class="p">-</span><span class="m" style="color: #099;">314</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">expected</span> <span class="k" style="font-weight: 600;">to</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">much</span> <span class="n" style="color: #333;">effect</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">topologies</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span></span>
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866
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="mosel"><span class="n" style="color: #333;">Simon</span> <span class="n" style="color: #333;">Whelan</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span></span>
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867
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="mosel"></span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="mosel"></span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="mosel"></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.15</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2006</span></span>
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871
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="mosel"></span>
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872
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="mosel"><span class="n" style="color: #333;">evolverNSbranches</span> <span class="p">(</span><span class="n" style="color: #333;">simulation</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span></span>
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873
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">substitution</span><span class="p">).</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">after</span></span>
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874
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="mosel"><span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">b</span> <span class="p">(?),</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.15</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span></span>
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<td class="diff-line-num old old_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
875
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="mosel"><span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">abort</span> <span class="n" style="color: #333;">prematurely</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">corrected</span><span class="p">.</span></span>
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876
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">N</span><span class="p">.</span> <span class="n" style="color: #333;">Clark</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span></span>
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877
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="mosel"></span>
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878
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="mosel"></span>
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879
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.15</span><span class="p">,</span> <span class="n" style="color: #333;">January</span> <span class="m" style="color: #099;">2006</span></span>
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880
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
881
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="mosel"><span class="n" style="color: #333;">evolver</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">simulation</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">evolver</span> <span class="n" style="color: #333;">program</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span></span>
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882
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="mosel"><span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">b</span> <span class="p">(?),</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.15</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">serious</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span></span>
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883
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="mosel"><span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">nonsensible</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">has</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">internal</span></span>
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884
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="mosel"><span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">a</span> <span class="p">(</span><span class="n" style="color: #333;">which</span></span>
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885
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">correct</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">c</span> <span class="p">(</span><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">wrong</span><span class="p">).</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">don</span><span class="s1" style="color: #d14;">'t seem to have kept</span></span>
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886
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="mosel"><span class="s1" style="color: #d14;">3.14b to check whether it is in error. In this case, the smart idea</span></span>
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887
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="mosel"><span class="s1" style="color: #d14;">that led to the bug was the thought that no evolution occurs if the</span></span>
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888
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="mosel"><span class="s1" style="color: #d14;">branch length is 0 (or less than 1e-20, to be more precise). If the</span></span>
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889
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="mosel"><span class="s1" style="color: #d14;">branch length is 0, there is no need to evolve the sequence along the</span></span>
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890
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="mosel"><span class="s1" style="color: #d14;">branch, so I decided to copy the sequence at the start of the branch</span></span>
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891
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="mosel"><span class="s1" style="color: #d14;">to the node at the end of the branch. This would be fine, except that</span></span>
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892
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="mosel"><span class="s1" style="color: #d14;">I introduced a bug at the same time that caused the program to skip</span></span>
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893
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="mosel"><span class="s1" style="color: #d14;">generating sequences at all nodes that are descendents of the</span></span>
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894
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="mosel"><span class="s1" style="color: #d14;">zero-length branch. As a result, sequences at tips that are</span></span>
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895
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="mosel"><span class="s1" style="color: #d14;">descendents of the zero-length branch have no data. On some systems</span></span>
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896
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="mosel"><span class="s1" style="color: #d14;">the uninitialized space is initialized as 0, and then the sequences</span></span>
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897
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="mosel"><span class="s1" style="color: #d14;">will be printed out as consisting of all Ts (T is the first nucleotide</span></span>
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898
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="mosel"><span class="s1" style="color: #d14;">in my program).</span></span>
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899
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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900
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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901
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="mosel"><span class="s1" style="color: #d14;">At the same time, I also turned on the option of simulating data on</span></span>
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902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="mosel"><span class="s1" style="color: #d14;">random trees in evolver. You change fixtree=1 into 0, and recompile.</span></span>
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903
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="mosel"><span class="s1" style="color: #d14;">Then use MCbaseRandomTree.dat to simulate data instead of MCbase.dat:</span></span>
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904
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="mosel"><span class="s1" style="color: #d14;"> evolver 5 MCbaseRandomTree.dat</span></span>
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906
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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907
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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908
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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909
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.15, November 2005</span></span>
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910
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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911
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="mosel"><span class="s1" style="color: #d14;">mcmctree: This implements the MCMC algorithm of Yang and Rannala (2005</span></span>
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912
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="mosel"><span class="s1" style="color: #d14;">MBE) for estimating species divergence times using soft bounds. The</span></span>
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913
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="mosel"><span class="s1" style="color: #d14;">example file is in examples/SoftBound/. Look at the readme file and</span></span>
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914
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="mosel"><span class="s1" style="color: #d14;">see whether you can duplicate our results in the paper. Note that</span></span>
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915
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="mosel"><span class="s1" style="color: #d14;">this program works with DNA sequence data only, and assumes the</span></span>
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916
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="mosel"><span class="s1" style="color: #d14;">molecular clock (clock = 1). Note that assumption of the clock can</span></span>
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917
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="mosel"><span class="s1" style="color: #d14;">lead to seriously biased results if the clock is violated. Work is</span></span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="mosel"><span class="s1" style="color: #d14;">under way to relax the clock assumption. </span></span>
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919
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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920
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="mosel"><span class="s1" style="color: #d14;">yn00: Added three methods for estimating dS and dN: LWL85 (Li, Wu &</span></span>
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921
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="mosel"><span class="s1" style="color: #d14;">Luo 1985), LPB93 (Li 1993; Pamilo and Bianchi 1993), and LWL85m (Yang</span></span>
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922
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="mosel"><span class="s1" style="color: #d14;">2006 Computaional Molecular Evolution, Oxford University Press. Eqs.</span></span>
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923
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="mosel"><span class="s1" style="color: #d14;">2.12 & 2.13).</span></span>
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924
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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925
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml. Added example files for clade model C, in folder</span></span>
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926
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="mosel"><span class="s1" style="color: #d14;">examples/CladeModelC. Thanks for Joe Bielawski for preparing these.</span></span>
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927
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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928
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="mosel"><span class="s1" style="color: #d14;">Added a sequence data format, in which the numbers or frequencies of</span></span>
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929
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<pre style="margin: 0;">-<span id="LC929" class="line" lang="mosel"><span class="s1" style="color: #d14;">site patterns are inputed instead of the sequences. The format is</span></span>
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930
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="mosel"><span class="s1" style="color: #d14;">indicated by the option variable P on the first line of the data file,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="mosel"><span class="s1" style="color: #d14;">used in the same way as option variables I (for interleaved format)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="mosel"><span class="s1" style="color: #d14;">and S (for sequential format, which is the default). See the section</span></span>
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933
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="mosel"><span class="s1" style="color: #d14;">on sequence data format in the paml documentation for details. The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
934
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="mosel"><span class="s1" style="color: #d14;">old control variable readpattf for baseml and codeml is now deleted.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
935
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="mosel"><span class="s1" style="color: #d14;">You can also use evolver to simulate data using this format. Look at</span></span>
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936
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="mosel"><span class="s1" style="color: #d14;">the control files MCbase.dat, MCcodon.dat, and MCaa.dat. This format</span></span>
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<td class="diff-line-num old old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
937
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="mosel"><span class="s1" style="color: #d14;">is useful for very large data sets with >1M sites, when collapsing</span></span>
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<td class="diff-line-num old old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
938
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="mosel"><span class="s1" style="color: #d14;">sites into patterns can take a long time. </span></span>
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939
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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940
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
942
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<pre style="margin: 0;">-<span id="LC942" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.14b, May 2005</span></span>
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943
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
944
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="mosel"><span class="s1" style="color: #d14;">pamp crashes when there are more than 127 or 255 (depending on the</span></span>
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945
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="mosel"><span class="s1" style="color: #d14;">system) species in the data. The bug is due to my declaration of the</span></span>
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946
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="mosel"><span class="s1" style="color: #d14;">variable visit[] in the routine PathwayMP1 in pamp.c as char rather</span></span>
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947
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="mosel"><span class="s1" style="color: #d14;">than int. Another problem is that the formula used to calculate</span></span>
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948
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="mosel"><span class="s1" style="color: #d14;">distances under REV (GTR) is sometimes inapplicable and the program</span></span>
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949
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="mosel"><span class="s1" style="color: #d14;">prints out messages like "err: DistanceREV". I introduced some ad hoc</span></span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="mosel"><span class="s1" style="color: #d14;">way of dealing with the problem.</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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952
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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953
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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954
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.14b, April 2005</span></span>
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955
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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956
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="mosel"><span class="s1" style="color: #d14;">aaml (codeml with seqtype = 2): </span></span>
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957
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
958
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="mosel"><span class="s1" style="color: #d14;">Under the REV model (model = 9), codeml failed to print out the</span></span>
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959
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="mosel"><span class="s1" style="color: #d14;">estimated amino acid substitution rate matrix. This is fixed.</span></span>
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960
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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961
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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962
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="mosel"><span class="s1" style="color: #d14;">aaml (codeml with seqtype = 2 or 3):</span></span>
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963
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<pre style="margin: 0;">-<span id="LC963" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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964
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="mosel"><span class="s1" style="color: #d14;">If you have multiple data sets (ndata > 1) and analysing protein data</span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="mosel"><span class="s1" style="color: #d14;">sets under the empirical models such as wag, jtt, dayhoff. The</span></span>
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966
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="mosel"><span class="s1" style="color: #d14;">results for the first data set are correct, but all later data sets</span></span>
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967
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="mosel"><span class="s1" style="color: #d14;">are analyzed incorrectly under the corresponding +F models, that is,</span></span>
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968
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<pre style="margin: 0;">-<span id="LC968" class="line" lang="mosel"><span class="s1" style="color: #d14;">wag+F, jtt+F, dayhoff+F. A bug in the program means that for the</span></span>
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969
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="mosel"><span class="s1" style="color: #d14;">second and later data sets, the equilibrium amino acid frequencies are</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="mosel"><span class="s1" style="color: #d14;">from the real data and not correctly set to those specified by the</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="mosel"><span class="s1" style="color: #d14;">empirical models. Thanks to Ben Evans.</span></span>
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972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.14b, February 2005</span></span>
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975
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<pre style="margin: 0;">-<span id="LC975" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml and aaml:</span></span>
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977
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<pre style="margin: 0;">-<span id="LC977" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
978
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="mosel"><span class="s1" style="color: #d14;">There is a bug that affects the joint reconstruction of ancestral</span></span>
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<td class="diff-line-num old old_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="mosel"><span class="s1" style="color: #d14;">sequences when some branch lengths are equal to each other and when</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="mosel"><span class="s1" style="color: #d14;">those branches are visited one after the other in the program. For</span></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="mosel"><span class="s1" style="color: #d14;">example, if some branch lengths are estimated to be 0, such a problem</span></span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="mosel"><span class="s1" style="color: #d14;">might occur. I think this bug is in the program for a long time,</span></span>
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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="mosel"><span class="s1" style="color: #d14;">although I note that joint ancestral reconstruction is turned off in</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="mosel"><span class="s1" style="color: #d14;">some versions for other reasons. The marginal reconstruction is not</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="mosel"><span class="s1" style="color: #d14;">affected by this bug. The update fixes this bug.</span></span>
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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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988
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml and codeml:</span></span>
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989
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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990
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="mosel"><span class="s1" style="color: #d14;">The program crashes on some systems for the local clock models (clock</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="mosel"><span class="s1" style="color: #d14;">= 5 and 6) after the calculation is finished. If you manage to run</span></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="mosel"><span class="s1" style="color: #d14;">the model, the results should be fine. There are bugs in the program</span></span>
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993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="mosel"><span class="s1" style="color: #d14;">when freeing memory at the end of the calculation. They are fixed in</span></span>
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994
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="mosel"><span class="s1" style="color: #d14;">this update. See the discussion site at</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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996
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="mosel"><span class="s1" style="color: #d14;">http://www.rannala.org/phpBB2/viewtopic.php?t=228</span></span>
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997
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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998
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="mosel"><span class="s1" style="color: #d14;">Thanks to fjvera.</span></span>
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999
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1000
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1001
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.14a, December 2004</span></span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml for codons):</span></span>
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1005
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="mosel"><span class="s1" style="color: #d14;">The mechanisctic amino acid substitution models (table 3 in Yang et</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="mosel"><span class="s1" style="color: #d14;">al. 1998 MBBE 15: 1600-1611) appear to be broken in paml/codeml</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="mosel"><span class="s1" style="color: #d14;">versions 3.13 and 3.14. They were correct in version 3.12. This is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="mosel"><span class="s1" style="color: #d14;">now fixed. If you use those models, please run the examples in the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="mosel"><span class="s1" style="color: #d14;">folder examples/mtCDNA/ and compare results with those published in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="mosel"><span class="s1" style="color: #d14;">the paper to confirm the program. The results in the paper are</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="mosel"><span class="s1" style="color: #d14;">correct, but the program implementation may be broken due to lack of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="mosel"><span class="s1" style="color: #d14;">maintenance.</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml for codons)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="mosel"><span class="s1" style="color: #d14;">When you fit the branch models with three or more branch types (omega</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="mosel"><span class="s1" style="color: #d14;">ratios), the program aborts with an error message saying that only two</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="mosel"><span class="s1" style="color: #d14;">omega ratios are allowed. This is due to a bug in the program and is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="mosel"><span class="s1" style="color: #d14;">now fixed.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1022
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1023
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.14, September 2004</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1025
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1026
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="mosel"><span class="s1" style="color: #d14;">1. codonml (codeml for codons): </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1027
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="mosel"><span class="s1" style="color: #d14;">(1a) NSsites models M1 (neutral), M2 (selection), and M8 (beta& ) have</span></span>
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1029
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="mosel"><span class="s1" style="color: #d14;">been changed. The references are two manuscripts that are not yet</span></span>
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1030
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="mosel"><span class="s1" style="color: #d14;">published (Wong, Yang, Goldman & Nielsen, 2004 Genetics 168:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1031
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="mosel"><span class="s1" style="color: #d14;">1041-1051; Yang, Wong, and Nielsen 2005 MBE). The details are as in the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1032
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="mosel"><span class="s1" style="color: #d14;">following table.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1033
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1034
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="mosel"><span class="s1" style="color: #d14;">[table missing or never written.]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1035
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1035" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1036
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="mosel"><span class="s1" style="color: #d14;">The old models M1 and M2 are noted to be rather unrealistic as they do</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1037
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1037" class="line" lang="mosel"><span class="s1" style="color: #d14;">not account for sites with 0 < w0 < 1. Thus in the new models 0 < w0 < 1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="mosel"><span class="s1" style="color: #d14;">is estimated from the data. Also insisting on a class of sites with 0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1039
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="mosel"><span class="s1" style="color: #d14;">= 1 appears to help avoid false positives as sites under weak</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1040
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="mosel"><span class="s1" style="color: #d14;">selection will be absorbed in this neutral class rather than being</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="mosel"><span class="s1" style="color: #d14;">claimed to be under positive selection. Under M8, the constraint s ></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="mosel"><span class="s1" style="color: #d14;">1 is now automatically enforced to help avoid multiple local peaks and</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="mosel"><span class="s1" style="color: #d14;">also to make the model a positive-selection model. Note that the</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="mosel"><span class="s1" style="color: #d14;">newer models replace the old ones, which are available in older</span></span>
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1045
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<pre style="margin: 0;">-<span id="LC1045" class="line" lang="mosel"><span class="s1" style="color: #d14;">versions of paml/codeml only.</span></span>
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1046
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<pre style="margin: 0;">-<span id="LC1046" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1047
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<pre style="margin: 0;">-<span id="LC1047" class="line" lang="mosel"><span class="s1" style="color: #d14;">After the changes, the models are nested as follows: M0 (one ratio) <</span></span>
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1048
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<pre style="margin: 0;">-<span id="LC1048" class="line" lang="mosel"><span class="s1" style="color: #d14;">M1a (NearlyNeutral) < M2a (PositiveSelection) < M3 (discrete), and M7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1049
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="mosel"><span class="s1" style="color: #d14;">(beta) < M8 (beta& ), where "<" means the model on the left is a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1050
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="mosel"><span class="s1" style="color: #d14;">special case of the model on the right:. Two LRTs can be constructed</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1051
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<pre style="margin: 0;">-<span id="LC1051" class="line" lang="mosel"><span class="s1" style="color: #d14;">using those models. The first one compares M1a against M2a, using a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1052
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<pre style="margin: 0;">-<span id="LC1052" class="line" lang="mosel"><span class="s1" style="color: #d14;">chi square with df 2, and the second one compares M7 against M8, using</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1053
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<pre style="margin: 0;">-<span id="LC1053" class="line" lang="mosel"><span class="s1" style="color: #d14;">a chi square with d.f. = 2.</span></span>
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1054
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<pre style="margin: 0;">-<span id="LC1054" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1055
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<pre style="margin: 0;">-<span id="LC1055" class="line" lang="mosel"><span class="s1" style="color: #d14;">(1b) Similarly branch-site model A (Yang and Nielsen 2002) is changed.</span></span>
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1056
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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="mosel"><span class="s1" style="color: #d14;">The old model assumes 0 = 0 and is unrealistic. This is replaced by 0</span></span>
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1057
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<pre style="margin: 0;">-<span id="LC1057" class="line" lang="mosel"><span class="s1" style="color: #d14;">< 0 < 1, estimated from the data. The new model is still called</span></span>
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1058
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<pre style="margin: 0;">-<span id="LC1058" class="line" lang="mosel"><span class="s1" style="color: #d14;">branch-site model A. It can be compared with the new M1a</span></span>
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1059
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<pre style="margin: 0;">-<span id="LC1059" class="line" lang="mosel"><span class="s1" style="color: #d14;">(NearlyNeutral) to form a likelihood ratio test, with d.f. 2. This</span></span>
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1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="mosel"><span class="s1" style="color: #d14;">is called test 1. Another test, called test 2, uses a null model A</span></span>
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1061
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<pre style="margin: 0;">-<span id="LC1061" class="line" lang="mosel"><span class="s1" style="color: #d14;">but with 2 = 1 fixed (use fix_omega = 1 and omega = 1). Test 2 is</span></span>
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1062
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<pre style="margin: 0;">-<span id="LC1062" class="line" lang="mosel"><span class="s1" style="color: #d14;">very conservative, but test 1 might mistake relaxed selective</span></span>
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1063
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<pre style="margin: 0;">-<span id="LC1063" class="line" lang="mosel"><span class="s1" style="color: #d14;">constraint on the foreground branch as positive selection.</span></span>
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1064
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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1065
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<pre style="margin: 0;">-<span id="LC1065" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1066
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<pre style="margin: 0;">-<span id="LC1066" class="line" lang="mosel"><span class="s1" style="color: #d14;">(1c) Similarly the clade model C ( see also Forsberg and Christiansen</span></span>
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1067
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<pre style="margin: 0;">-<span id="LC1067" class="line" lang="mosel"><span class="s1" style="color: #d14;">2003; Bielawski and Yang 2004) is changed as follows. The new model C</span></span>
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1068
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<pre style="margin: 0;">-<span id="LC1068" class="line" lang="mosel"><span class="s1" style="color: #d14;">replaces 0 = 0 by 0 < 0 < 1 and has five parameters in the</span></span>
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1069
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<pre style="margin: 0;">-<span id="LC1069" class="line" lang="mosel"><span class="s1" style="color: #d14;">distribution: p0, p1, 0, 2, and 3. The new model C can be compared</span></span>
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1070
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<pre style="margin: 0;">-<span id="LC1070" class="line" lang="mosel"><span class="s1" style="color: #d14;">with the new M1a (NearlyNeutral), with d.f. 3.</span></span>
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1071
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<pre style="margin: 0;">-<span id="LC1071" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1072
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<pre style="margin: 0;">-<span id="LC1072" class="line" lang="mosel"><span class="s1" style="color: #d14;">(1d) The empirical Bayes procedure for calculating posterior</span></span>
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1073
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="mosel"><span class="s1" style="color: #d14;">probabilities of site classes under the site models, branch-site</span></span>
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1074
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<pre style="margin: 0;">-<span id="LC1074" class="line" lang="mosel"><span class="s1" style="color: #d14;">models, and clade models are called naïve empirical Bayes (NEB). They</span></span>
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1075
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<pre style="margin: 0;">-<span id="LC1075" class="line" lang="mosel"><span class="s1" style="color: #d14;">are naïve because they use the MLEs of parameters without accounting</span></span>
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1076
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<pre style="margin: 0;">-<span id="LC1076" class="line" lang="mosel"><span class="s1" style="color: #d14;">for sampling errors in them. This problem is now fixed using a</span></span>
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1077
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<pre style="margin: 0;">-<span id="LC1077" class="line" lang="mosel"><span class="s1" style="color: #d14;">procedure called Bayes empirical Bayes (BEB) (Yang, Wong, and Nielsen</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="mosel"><span class="s1" style="color: #d14;">2005). The BEB procedure is implemented for the site models M2a and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1079
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="mosel"><span class="s1" style="color: #d14;">M8, the (modified) branch-site model A, and the (modified) clade model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1080
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<pre style="margin: 0;">-<span id="LC1080" class="line" lang="mosel"><span class="s1" style="color: #d14;">C. The old NEB calculation is kept in the output and the new BEB</span></span>
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1081
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<pre style="margin: 0;">-<span id="LC1081" class="line" lang="mosel"><span class="s1" style="color: #d14;">results follow the NEB result. Perhaps I will remove the NEB</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1082
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1082" class="line" lang="mosel"><span class="s1" style="color: #d14;">calculation in later versions.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1083
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1083" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1084
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1084" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1085
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1085" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml/codeml: rewrote likelihood clock and local clock models.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1086
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<pre style="margin: 0;">-<span id="LC1086" class="line" lang="mosel"><span class="s1" style="color: #d14;">Implemented models for combined analysis of multiple genes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1087
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1087" class="line" lang="mosel"><span class="s1" style="color: #d14;">incorporating multiple calibration points (Yang and Yoder 2003). The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1088
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1088" class="line" lang="mosel"><span class="s1" style="color: #d14;">ad hoc rate smoothing procedure of Yang (2004) is implemented for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1089
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1089" class="line" lang="mosel"><span class="s1" style="color: #d14;">nucleotide, amino acid, and codon substitution models, and the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1090
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<pre style="margin: 0;">-<span id="LC1090" class="line" lang="mosel"><span class="s1" style="color: #d14;">implementation also deals with missing species at some loci. The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1091
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="mosel"><span class="s1" style="color: #d14;">option variable clock in the control files is now used differently</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1092
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<pre style="margin: 0;">-<span id="LC1092" class="line" lang="mosel"><span class="s1" style="color: #d14;">from before. See later in this documentation and also the readme and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1093
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<pre style="margin: 0;">-<span id="LC1093" class="line" lang="mosel"><span class="s1" style="color: #d14;">readme2 files in the folder examples/MouseLemurs/.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1094
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1095
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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml/codeml local clock models. clock = 5 and 6 are added in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1096
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<pre style="margin: 0;">-<span id="LC1096" class="line" lang="mosel"><span class="s1" style="color: #d14;">3.14beta5.</span></span>
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1097
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<pre style="margin: 0;">-<span id="LC1097" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1098
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<pre style="margin: 0;">-<span id="LC1098" class="line" lang="mosel"><span class="s1" style="color: #d14;">codeml: added branch-site models C and D (Bielawski and Yang in press).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1099
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<pre style="margin: 0;">-<span id="LC1099" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1100
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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="mosel"><span class="s1" style="color: #d14;">mcmctree: this program is disabled in this release. The old program</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="mosel"><span class="s1" style="color: #d14;">died and the new program is still under construction.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="mosel"><span class="s1" style="color: #d14;">The main body of this documentation may not be up to date. </span></span>
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1104
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<pre style="margin: 0;">-<span id="LC1104" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1105
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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1106
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1107
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="mosel"><span class="s1" style="color: #d14;">Bug fixes and minor corrections</span></span>
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1108
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<pre style="margin: 0;">-<span id="LC1108" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1109
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<pre style="margin: 0;">-<span id="LC1109" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1110
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<pre style="margin: 0;">-<span id="LC1110" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml/codeml. The output in the file rates under the gamma model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1111
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="mosel"><span class="s1" style="color: #d14;">lists inferred rate for each site. The output is incorrect if the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1112
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<pre style="margin: 0;">-<span id="LC1112" class="line" lang="mosel"><span class="s1" style="color: #d14;">tree is large and scaling is used to avoid underflow. The use of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1113
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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="mosel"><span class="s1" style="color: #d14;">scaling is indicated by two lines of output on the monitor like the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1114
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<pre style="margin: 0;">-<span id="LC1114" class="line" lang="mosel"><span class="s1" style="color: #d14;">following:</span></span>
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1115
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1116
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<pre style="margin: 0;">-<span id="LC1116" class="line" lang="mosel"><span class="s1" style="color: #d14;">"2 node(s) used for scaling (Yang 2000 J Mol Evol 51:423-432):</span></span>
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1117
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<pre style="margin: 0;">-<span id="LC1117" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 155 350". </span></span>
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1118
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<pre style="margin: 0;">-<span id="LC1118" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1119
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<pre style="margin: 0;">-<span id="LC1119" class="line" lang="mosel"><span class="s1" style="color: #d14;">The results are clearly wrong as the probabilities are much greater</span></span>
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1120
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<pre style="margin: 0;">-<span id="LC1120" class="line" lang="mosel"><span class="s1" style="color: #d14;">than 1, and the rates are many orders of magnitude too large, etc.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1121
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="mosel"><span class="s1" style="color: #d14;">Also under the same problematic condition the expected numbers of</span></span>
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1122
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="mosel"><span class="s1" style="color: #d14;">sites with certain site patterns in the file lnf are incorrect. When</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1123
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="mosel"><span class="s1" style="color: #d14;">scaling is not used, the results should be o.k. and look reasonable.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1124
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="mosel"><span class="s1" style="color: #d14;">This affects versions 3.13 and 3.14beta1-3. This is fixed in version</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1125
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<pre style="margin: 0;">-<span id="LC1125" class="line" lang="mosel"><span class="s1" style="color: #d14;">3.14. Thanks for Nick Goldman for pointing out the error.</span></span>
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1126
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<pre style="margin: 0;">-<span id="LC1126" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1127
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<pre style="margin: 0;">-<span id="LC1127" class="line" lang="mosel"><span class="s1" style="color: #d14;">yn00. The program crashes for large datasets with many codons due to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1128
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<pre style="margin: 0;">-<span id="LC1128" class="line" lang="mosel"><span class="s1" style="color: #d14;">a memory allocation error. This affects versions 3.13 and some</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1129
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1129" class="line" lang="mosel"><span class="s1" style="color: #d14;">versions of 3.14beta1. The problem is fixed in version 3.14.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1130
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<pre style="margin: 0;">-<span id="LC1130" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1131
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<pre style="margin: 0;">-<span id="LC1131" class="line" lang="mosel"><span class="s1" style="color: #d14;">aaml (codeml for amino acids). Model REVaa_0 is broken due to lack of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1132
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1132" class="line" lang="mosel"><span class="s1" style="color: #d14;">maintenance in versions 3.1, 3.11, 3,12, 3,13, and 3,14beta1-4. It</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1133
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1133" class="line" lang="mosel"><span class="s1" style="color: #d14;">seems to be working in version 3. This is fixed in 3.14beta5. 2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1134
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<pre style="margin: 0;">-<span id="LC1134" class="line" lang="mosel"><span class="s1" style="color: #d14;">April 2004.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1135
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1136
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml for codons) in branch-site models (model = 2 NSsites =</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1137
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="mosel"><span class="s1" style="color: #d14;">2 or 3) prior to 3.14beta3 have a scaling problem, which makes the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1138
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="mosel"><span class="s1" style="color: #d14;">length of the foreground branch to be incorrectly estimated. Other</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="mosel"><span class="s1" style="color: #d14;">branch lengths and substitution parameters, such as the parameters in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1140
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<pre style="margin: 0;">-<span id="LC1140" class="line" lang="mosel"><span class="s1" style="color: #d14;">the distribution, are corrected calculated, as well as the log</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1141
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<pre style="margin: 0;">-<span id="LC1141" class="line" lang="mosel"><span class="s1" style="color: #d14;">likelihood values and the posterior probabilities. 27 March 2004</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1142
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<pre style="margin: 0;">-<span id="LC1142" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1143
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<pre style="margin: 0;">-<span id="LC1143" class="line" lang="mosel"><span class="s1" style="color: #d14;">pamp: The gamma parameter for variable rates among sites using the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1144
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="mosel"><span class="s1" style="color: #d14;">method of Yang & Kumar (1996) is not estimated correctly in 3.14beta1,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1145
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1145" class="line" lang="mosel"><span class="s1" style="color: #d14;">beta2, beta3. Versions 3.13d and earlier seem fine.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1146
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<pre style="margin: 0;">-<span id="LC1146" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1147
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1147" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml for codons) in version 3.14beta and 3.14beta1 does not</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1148
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1148" class="line" lang="mosel"><span class="s1" style="color: #d14;">work when fix_omega = 1 is used for branch models. The results are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1149
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1149" class="line" lang="mosel"><span class="s1" style="color: #d14;">incorrect. Please use newer versions 3.14beta3 or later. Also</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1150
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1150" class="line" lang="mosel"><span class="s1" style="color: #d14;">version 3.13 is fine.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1151
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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1152
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<pre style="margin: 0;">-<span id="LC1152" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml: Models TN93 and REV are wrong when used with Mgene = 3 or 4.</span></span>
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1153
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<pre style="margin: 0;">-<span id="LC1153" class="line" lang="mosel"><span class="s1" style="color: #d14;">This seems correct in version 3.12 but went wrong in 3.13 and 3.14</span></span>
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1154
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<pre style="margin: 0;">-<span id="LC1154" class="line" lang="mosel"><span class="s1" style="color: #d14;">since I inserted TN92 between HKY85 and TN93. Thanks for Lee Bofkin</span></span>
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1155
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<pre style="margin: 0;">-<span id="LC1155" class="line" lang="mosel"><span class="s1" style="color: #d14;">for reporting the error.</span></span>
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1156
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<pre style="margin: 0;">-<span id="LC1156" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1157
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<pre style="margin: 0;">-<span id="LC1157" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml for codons): When codon models are used to reconstruct</span></span>
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1158
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<pre style="margin: 0;">-<span id="LC1158" class="line" lang="mosel"><span class="s1" style="color: #d14;">ancestral sequences (with RateAncestor = 1), the program lists</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1159
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<pre style="margin: 0;">-<span id="LC1159" class="line" lang="mosel"><span class="s1" style="color: #d14;">synonymous and nonsynonymous changes at each site under the heading</span></span>
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1160
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<pre style="margin: 0;">-<span id="LC1160" class="line" lang="mosel"><span class="s1" style="color: #d14;">"Changes at sites (syn nonsyn)." This listing is incorrect due to a</span></span>
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1161
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<pre style="margin: 0;">-<span id="LC1161" class="line" lang="mosel"><span class="s1" style="color: #d14;">bug in the program. This bug affects versions 3.12, 3.13 and 3.14,</span></span>
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1162
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<pre style="margin: 0;">-<span id="LC1162" class="line" lang="mosel"><span class="s1" style="color: #d14;">and version 3.11 seems correct. Thanks to Joe Bielawski.</span></span>
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1163
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<pre style="margin: 0;">-<span id="LC1163" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1164
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<pre style="margin: 0;">-<span id="LC1164" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml/codeml: The SE'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">divergence</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span></span>
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1165
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<pre style="margin: 0;">-<span id="LC1165" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">calculated</span> <span class="n" style="color: #333;">incorrectly</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">happens</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">2</span><span class="p">,</span></span>
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1166
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<pre style="margin: 0;">-<span id="LC1166" class="line" lang="mosel"><span class="n" style="color: #333;">supply</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">date</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">calculate</span> <span class="n" style="color: #333;">absolute</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">request</span> <span class="n" style="color: #333;">standard</span></span>
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1167
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="mosel"><span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">estimates</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">themselves</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="n" style="color: #333;">but</span></span>
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1168
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<pre style="margin: 0;">-<span id="LC1168" class="line" lang="mosel"><span class="n" style="color: #333;">standard</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">wrong</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">SEs</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span></span>
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1169
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<pre style="margin: 0;">-<span id="LC1169" class="line" lang="mosel"><span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">TipDate</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">wrong</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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1170
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<pre style="margin: 0;">-<span id="LC1170" class="line" lang="mosel"><span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">print</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variances</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">the</span> <span class="p">+-,</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">square</span></span>
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1171
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<pre style="margin: 0;">-<span id="LC1171" class="line" lang="mosel"><span class="n" style="color: #333;">roots</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.13</span><span class="p">.</span> <span class="n" style="color: #333;">Versions</span> <span class="n" style="color: #333;">prior</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1172
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1172" class="line" lang="mosel"><span class="m" style="color: #099;">3.13</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">posted</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">update</span> <span class="m" style="color: #099;">3.13</span><span class="n" style="color: #333;">d</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">fix</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span></span>
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1173
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1174
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1174" class="line" lang="mosel"><span class="n" style="color: #333;">evolver</span><span class="p">:</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">simulation</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">accept</span> <span class="n" style="color: #333;">species</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1175
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1175" class="line" lang="mosel"><span class="n" style="color: #333;">tree</span><span class="p">.</span> <span class="n" style="color: #333;">Note</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">formats</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">evolver</span> <span class="p">(</span><span class="n" style="color: #333;">MCbase</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1176
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1176" class="line" lang="mosel"><span class="n" style="color: #333;">MCcodon</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span> <span class="n" style="color: #333;">MCaa</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">)</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">changed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">might</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">your</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1177
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1177" class="line" lang="mosel"><span class="n" style="color: #333;">own</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">files</span><span class="p">.</span> <span class="n" style="color: #333;">Look</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">package</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1178
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1178" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1179
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1179" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">documentation</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">paml</span> <span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.13</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">August</span> <span class="m" style="color: #099;">2002</span> <span class="p">-</span> <span class="m" style="color: #099;">12</span> <span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2002</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1180
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1180" class="line" lang="mosel"><span class="n" style="color: #333;">had</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">mistake</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">critical</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">newer</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1181
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1181" class="line" lang="mosel"><span class="n" style="color: #333;">modified</span> <span class="n" style="color: #333;">M8</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">critical</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">are</span> <span class="m" style="color: #099;">2.71</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="m" style="color: #099;">5</span><span class="p">%</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1182
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1182" class="line" lang="mosel"><span class="n" style="color: #333;">significance</span> <span class="n" style="color: #333;">level</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">5.41</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="m" style="color: #099;">1</span><span class="p">%</span> <span class="n" style="color: #333;">level</span><span class="p">,</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">1.95</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.32</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1183
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1183" class="line" lang="mosel"><span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1184
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<pre style="margin: 0;">-<span id="LC1184" class="line" lang="mosel"></span>
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1185
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<pre style="margin: 0;">-<span id="LC1185" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1186
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1187
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="mosel"></span>
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1188
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1189
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">beta2</span><span class="p">,</span> <span class="n" style="color: #333;">November</span> <span class="m" style="color: #099;">2003</span></span>
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1190
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<pre style="margin: 0;">-<span id="LC1190" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1191
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<pre style="margin: 0;">-<span id="LC1191" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">baseml</span><span class="p">:</span> <span class="n" style="color: #333;">Models</span> <span class="n" style="color: #333;">TN93</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">REV</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">wrong</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Mgene</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">or</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1192
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<pre style="margin: 0;">-<span id="LC1192" class="line" lang="mosel"> <span class="m" style="color: #099;">4.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">seems</span> <span class="n" style="color: #333;">correct</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.12</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">went</span> <span class="n" style="color: #333;">wrong</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">3.13</span> <span class="k" style="font-weight: 600;">and</span></span>
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1193
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<pre style="margin: 0;">-<span id="LC1193" class="line" lang="mosel"> <span class="m" style="color: #099;">3.14</span> <span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">inserted</span> <span class="n" style="color: #333;">TN92</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">HKY85</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">TN93</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Lee</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1194
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<pre style="margin: 0;">-<span id="LC1194" class="line" lang="mosel"> <span class="n" style="color: #333;">Bofkin</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reporting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">error</span><span class="p">.</span></span>
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1195
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<pre style="margin: 0;">-<span id="LC1195" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1196
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">codonml</span> <span class="p">(</span><span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">codons</span><span class="p">):</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1197
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="mosel"> <span class="n" style="color: #333;">reconstruct</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">sequences</span> <span class="p">(</span><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">RateAncestor</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1198
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<pre style="margin: 0;">-<span id="LC1198" class="line" lang="mosel"> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">lists</span> <span class="n" style="color: #333;">synonymous</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nonsynonymous</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">site</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1199
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<pre style="margin: 0;">-<span id="LC1199" class="line" lang="mosel"> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">heading</span> <span class="s2" style="color: #d14;">"Changes at sites (syn nonsyn)."</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">listing</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1200
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<pre style="margin: 0;">-<span id="LC1200" class="line" lang="mosel"> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">incorrect</span> <span class="n" style="color: #333;">due</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">affects</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1201
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<pre style="margin: 0;">-<span id="LC1201" class="line" lang="mosel"> <span class="n" style="color: #333;">versions</span> <span class="m" style="color: #099;">3.12</span><span class="p">,</span> <span class="m" style="color: #099;">3.13</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.14</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.11</span> <span class="n" style="color: #333;">seems</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1202
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<pre style="margin: 0;">-<span id="LC1202" class="line" lang="mosel"> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Joe</span> <span class="n" style="color: #333;">Bielawski</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1203
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<pre style="margin: 0;">-<span id="LC1203" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1204
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1204" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1205
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1205" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1206
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1206" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.14</span><span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="m" style="color: #099;">20</span> <span class="n" style="color: #333;">July</span> <span class="m" style="color: #099;">2003</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1207
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<pre style="margin: 0;">-<span id="LC1207" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1208
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">baseml</span><span class="p">/</span><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">rewrote</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span><span class="p">.</span></span>
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1209
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<pre style="margin: 0;">-<span id="LC1209" class="line" lang="mosel"> <span class="n" style="color: #333;">Implemented</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">combined</span> <span class="n" style="color: #333;">analysis</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">genes</span> <span class="n" style="color: #333;">using</span></span>
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1210
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<pre style="margin: 0;">-<span id="LC1210" class="line" lang="mosel"> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">points</span> <span class="p">(</span><span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yoder</span> <span class="m" style="color: #099;">2003</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">option</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1211
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<pre style="margin: 0;">-<span id="LC1211" class="line" lang="mosel"> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">differently</span> <span class="k" style="font-weight: 600;">from</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1212
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1212" class="line" lang="mosel"> <span class="n" style="color: #333;">before</span><span class="p">.</span> <span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">documentation</span> <span class="n" style="color: #333;">below</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">readme</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">example</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1213
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<pre style="margin: 0;">-<span id="LC1213" class="line" lang="mosel"> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">folder</span> <span class="n" style="color: #333;">paml</span><span class="p">/</span><span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">MouseLemurs</span><span class="p">/.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1214
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<pre style="margin: 0;">-<span id="LC1214" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1215
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1215" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">branch</span><span class="p">-</span><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">C</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">D</span> <span class="p">(</span><span class="n" style="color: #333;">Bielawski</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1216
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1216" class="line" lang="mosel"> <span class="n" style="color: #333;">submitted</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1217
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<pre style="margin: 0;">-<span id="LC1217" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1218
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1218" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">baseml</span><span class="p">/</span><span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">SE</span><span class="s1" style="color: #d14;">'s for divergence times under the clock</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1219
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<pre style="margin: 0;">-<span id="LC1219" class="line" lang="mosel"><span class="s1" style="color: #d14;"> models are calculated incorrectly. This happens when you use clock</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1220
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<pre style="margin: 0;">-<span id="LC1220" class="line" lang="mosel"><span class="s1" style="color: #d14;"> = 1 or 2, supply fossil date to calculate absolute times, and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1221
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<pre style="margin: 0;">-<span id="LC1221" class="line" lang="mosel"><span class="s1" style="color: #d14;"> request standard errors for times. The estimates of times</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1222
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<pre style="margin: 0;">-<span id="LC1222" class="line" lang="mosel"><span class="s1" style="color: #d14;"> themselves are correct, but standard errors for times are wrong.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1223
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<pre style="margin: 0;">-<span id="LC1223" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The SEs for times and for the rate under the TipDate model (clock =</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1224
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<pre style="margin: 0;">-<span id="LC1224" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 3) are wrong as well. The programs print out the variances after</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1225
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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the +-, instead of their square roots. This error was introduced</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1226
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<pre style="margin: 0;">-<span id="LC1226" class="line" lang="mosel"><span class="s1" style="color: #d14;"> in version 3.13. Versions prior to 3.13 are correct. I posted an</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1227
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<pre style="margin: 0;">-<span id="LC1227" class="line" lang="mosel"><span class="s1" style="color: #d14;"> update 3.13d to fix this bug.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1228
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<pre style="margin: 0;">-<span id="LC1228" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1229
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<pre style="margin: 0;">-<span id="LC1229" class="line" lang="mosel"><span class="s1" style="color: #d14;">(4) mcmctree: this program is decommissioned in this release. The old</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1230
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<pre style="margin: 0;">-<span id="LC1230" class="line" lang="mosel"><span class="s1" style="color: #d14;"> program died and the new program is still under construction.</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1232
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<pre style="margin: 0;">-<span id="LC1232" class="line" lang="mosel"><span class="s1" style="color: #d14;">(5) evolver: the simulation program can now accept species names in</span></span>
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1233
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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the tree. Note that the data file formats for evolver (MCbase.dat,</span></span>
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1234
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<pre style="margin: 0;">-<span id="LC1234" class="line" lang="mosel"><span class="s1" style="color: #d14;"> MCcodon.dat, MCaa.dat) have changed and you might have to change</span></span>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="mosel"><span class="s1" style="color: #d14;"> your own data files. Look at the files included in the package.</span></span>
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1236
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<pre style="margin: 0;">-<span id="LC1236" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1237
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<pre style="margin: 0;">-<span id="LC1237" class="line" lang="mosel"><span class="s1" style="color: #d14;">(6) Improved the iteration algorithm a little. No change to the</span></span>
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1238
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<pre style="margin: 0;">-<span id="LC1238" class="line" lang="mosel"><span class="s1" style="color: #d14;"> interface.</span></span>
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1239
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<pre style="margin: 0;">-<span id="LC1239" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1240
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<pre style="margin: 0;">-<span id="LC1240" class="line" lang="mosel"><span class="s1" style="color: #d14;">(7) The documentation in paml v3.13 from August 2002 - 12 December</span></span>
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1241
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<pre style="margin: 0;">-<span id="LC1241" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 2002 had a mistake about the critical values for the newer test</span></span>
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1242
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<pre style="margin: 0;">-<span id="LC1242" class="line" lang="mosel"><span class="s1" style="color: #d14;"> using a modified M8. The critical values for the test are 2.71 at</span></span>
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1243
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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the 5% significance level and 5.41 at the 1% level, rather than</span></span>
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1244
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<pre style="margin: 0;">-<span id="LC1244" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 1.95 and 3.32 as in the documentation.</span></span>
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1245
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<pre style="margin: 0;">-<span id="LC1245" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1246
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<pre style="margin: 0;">-<span id="LC1246" class="line" lang="mosel"><span class="s1" style="color: #d14;">(8) Edited the manual pamlDOC.pdf.</span></span>
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1247
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<pre style="margin: 0;">-<span id="LC1247" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1248
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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1249
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<pre style="margin: 0;">-<span id="LC1249" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1250
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<pre style="margin: 0;">-<span id="LC1250" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1251
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<pre style="margin: 0;">-<span id="LC1251" class="line" lang="mosel"><span class="s1" style="color: #d14;">15 May 2003</span></span>
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1252
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<pre style="margin: 0;">-<span id="LC1252" class="line" lang="mosel"><span class="s1" style="color: #d14;">paml3.13d</span></span>
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1253
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<pre style="margin: 0;">-<span id="LC1253" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1254
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<pre style="margin: 0;">-<span id="LC1254" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml/codeml: The SE'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">are</span></span>
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1255
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<pre style="margin: 0;">-<span id="LC1255" class="line" lang="mosel"><span class="n" style="color: #333;">calculated</span> <span class="n" style="color: #333;">incorrectly</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">happens</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">2</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1256
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1256" class="line" lang="mosel"><span class="n" style="color: #333;">supply</span> <span class="n" style="color: #333;">fossil</span> <span class="n" style="color: #333;">date</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">calculate</span> <span class="n" style="color: #333;">absolute</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">request</span> <span class="n" style="color: #333;">standard</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1257
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1257" class="line" lang="mosel"><span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">estimates</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">themselves</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span><span class="p">,</span> <span class="n" style="color: #333;">but</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1258
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1258" class="line" lang="mosel"><span class="n" style="color: #333;">standard</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">wrong</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">SEs</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">times</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1259
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1259" class="line" lang="mosel"><span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">TipDate</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">wrong</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1260
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1260" class="line" lang="mosel"><span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">print</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variances</span> <span class="n" style="color: #333;">after</span> <span class="n" style="color: #333;">the</span> <span class="p">+-,</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">square</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1261
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1261" class="line" lang="mosel"><span class="n" style="color: #333;">roots</span><span class="p">.</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1262
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1262" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1263
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1263" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">introduced</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.13</span><span class="p">.</span> <span class="n" style="color: #333;">Versions</span> <span class="n" style="color: #333;">prior</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">3.13</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1264
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1264" class="line" lang="mosel"><span class="n" style="color: #333;">correct</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1265
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1265" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1266
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1266" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1267
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1267" class="line" lang="mosel"><span class="m" style="color: #099;">12</span> <span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2002</span> <span class="n" style="color: #333;">correction</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">documentation</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1268
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1268" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1269
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1269" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">paml</span> <span class="n" style="color: #333;">documentation</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">paml</span> <span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.13</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">August</span> <span class="m" style="color: #099;">2002</span> <span class="p">-</span> <span class="m" style="color: #099;">12</span> <span class="n" style="color: #333;">December</span> <span class="m" style="color: #099;">2002</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1270
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1270" class="line" lang="mosel"><span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">mistake</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">critical</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">newer</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1271
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1271" class="line" lang="mosel"><span class="n" style="color: #333;">modified</span> <span class="n" style="color: #333;">M8</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1272
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1272" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1273
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1273" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">critical</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">are</span> <span class="m" style="color: #099;">2.71</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="m" style="color: #099;">5</span><span class="p">%</span> <span class="n" style="color: #333;">significance</span> <span class="n" style="color: #333;">level</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1274
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<pre style="margin: 0;">-<span id="LC1274" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">5.41</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="m" style="color: #099;">1</span><span class="p">%</span> <span class="n" style="color: #333;">level</span><span class="p">,</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">1.95</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">3.32</span> <span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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1275
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<pre style="margin: 0;">-<span id="LC1275" class="line" lang="mosel"><span class="n" style="color: #333;">documentation</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">made</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">mistake</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">quickly</span> <span class="n" style="color: #333;">discovered</span> <span class="n" style="color: #333;">it</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">thought</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1276
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<pre style="margin: 0;">-<span id="LC1276" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">corrected</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">months</span> <span class="n" style="color: #333;">ago</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">apparently</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">document</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1277
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1277" class="line" lang="mosel"><span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">paml</span> <span class="n" style="color: #333;">release</span> <span class="n" style="color: #333;">had</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">mistake</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">am</span> <span class="n" style="color: #333;">sorry</span><span class="p">.</span> <span class="n" style="color: #333;">I</span><span class="s1" style="color: #d14;">'ll</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1278
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1278" class="line" lang="mosel"><span class="s1" style="color: #d14;">correct it now.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1279
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<pre style="margin: 0;">-<span id="LC1279" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1280
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<pre style="margin: 0;">-<span id="LC1280" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1281
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<pre style="margin: 0;">-<span id="LC1281" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1282
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<pre style="margin: 0;">-<span id="LC1282" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.13, August 2002</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1283
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<pre style="margin: 0;">-<span id="LC1283" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1284
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<pre style="margin: 0;">-<span id="LC1284" class="line" lang="mosel"><span class="s1" style="color: #d14;">(1) baseml: nhomo = 1 and model = 6 (for both the one-rate and gamma-rates</span></span>
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1285
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<pre style="margin: 0;">-<span id="LC1285" class="line" lang="mosel"><span class="s1" style="color: #d14;"> models) in version 3.12 gives incorrect results. The error was introduced </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1286
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<pre style="margin: 0;">-<span id="LC1286" class="line" lang="mosel"><span class="s1" style="color: #d14;"> in version 3.12 and is now fixed. Sorry for the trouble and thanks to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1287
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<pre style="margin: 0;">-<span id="LC1287" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Joshua Scott Rest.</span></span>
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1288
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<pre style="margin: 0;">-<span id="LC1288" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1289
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<pre style="margin: 0;">-<span id="LC1289" class="line" lang="mosel"><span class="s1" style="color: #d14;">(2) baseml: Tamura'</span><span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="m" style="color: #099;">1992</span><span class="p">)</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">inserted</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">HKY85</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">TN93</span><span class="p">.</span> </span>
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1290
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<pre style="margin: 0;">-<span id="LC1290" class="line" lang="mosel"> <span class="n" style="color: #333;">Unfortunately</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">TN93</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">REV</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">shifted</span><span class="p">,</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1291
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1291" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">also</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1292
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="mosel"> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">user</span><span class="p">-</span><span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">REV</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">UNREST</span> <span class="n" style="color: #333;">models</span><span class="p">.</span></span>
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1293
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<pre style="margin: 0;">-<span id="LC1293" class="line" lang="mosel"> <span class="m" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">JC69</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">K80</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">:</span><span class="n" style="color: #333;">F81</span><span class="p">,</span> <span class="m" style="color: #099;">3</span><span class="p">:</span><span class="n" style="color: #333;">F84</span><span class="p">,</span> <span class="m" style="color: #099;">4</span><span class="p">:</span><span class="n" style="color: #333;">HKY85</span><span class="p">,</span> <span class="m" style="color: #099;">5</span><span class="p">:</span><span class="n" style="color: #333;">T92</span><span class="p">,</span> <span class="m" style="color: #099;">6</span><span class="p">:</span><span class="n" style="color: #333;">TN93</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1294
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<pre style="margin: 0;">-<span id="LC1294" class="line" lang="mosel"> <span class="m" style="color: #099;">7</span><span class="p">:</span><span class="n" style="color: #333;">REV</span><span class="p">,</span> <span class="m" style="color: #099;">8</span><span class="p">:</span><span class="n" style="color: #333;">UNREST</span><span class="p">,</span> <span class="m" style="color: #099;">9</span><span class="p">:</span><span class="n" style="color: #333;">REVu</span><span class="p">;</span> <span class="m" style="color: #099;">10</span><span class="p">:</span><span class="n" style="color: #333;">UNRESTu</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1295
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1295" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1296
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1296" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nonhomogeneous</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Galtier</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Gouy</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1297
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="mosel"> <span class="p">(</span><span class="m" style="color: #099;">1998</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="k" style="font-weight: 600;">options</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">5</span> <span class="p">(</span><span class="n" style="color: #333;">T92</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nhomo</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> <span class="p">(</span><span class="n" style="color: #333;">N1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">4</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1298
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="mosel"> <span class="p">(</span><span class="n" style="color: #333;">N2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">5</span> <span class="p">(</span><span class="n" style="color: #333;">user</span><span class="p">).</span> <span class="n" style="color: #333;">nhomo</span> <span class="p">=</span> <span class="m" style="color: #099;">5</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1299
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1299" class="line" lang="mosel"> <span class="n" style="color: #333;">Roberts</span> <span class="p">(</span><span class="m" style="color: #099;">1995</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">specifies</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1300
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="mosel"> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">base</span> <span class="n" style="color: #333;">frequencies</span> <span class="p">(</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">GC</span> <span class="n" style="color: #333;">content</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1301
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">parameters</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Galtier</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Gouy</span> <span class="m" style="color: #099;">1998</span><span class="p">)</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1302
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<pre style="margin: 0;">-<span id="LC1302" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">branches</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">sets</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1303
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1303" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1304
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1304" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">5</span><span class="p">)</span> <span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">comparison</span> <span class="p">(</span><span class="n" style="color: #333;">seqtype</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1305
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1305" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">crashes</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">now</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1306
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<pre style="margin: 0;">-<span id="LC1306" class="line" lang="mosel"> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Dennis</span> <span class="n" style="color: #333;">Paul</span> <span class="n" style="color: #333;">Wall</span><span class="p">.</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1307
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1307" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1308
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1308" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">6</span><span class="p">)</span> <span class="n" style="color: #333;">codeml</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">mechanistic</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">substitution</span> <span class="p">(</span><span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">6</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">7</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1309
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<pre style="margin: 0;">-<span id="LC1309" class="line" lang="mosel"> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">quite</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">time</span> <span class="n" style="color: #333;">due</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">lack</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">maintenance</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span></span>
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1310
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<pre style="margin: 0;">-<span id="LC1310" class="line" lang="mosel"> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">them</span><span class="p">.</span> <span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">examples</span><span class="p">/</span><span class="n" style="color: #333;">mtCDNA</span><span class="p">/</span><span class="n" style="color: #333;">readme</span><span class="p">.</span><span class="n" style="color: #333;">txt</span><span class="p">.</span></span>
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1311
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<pre style="margin: 0;">-<span id="LC1311" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1312
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<pre style="margin: 0;">-<span id="LC1312" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">7</span><span class="p">)</span> <span class="n" style="color: #333;">codemlsites</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">removed</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">batch</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">NSsites</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1313
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1313" class="line" lang="mosel"> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">done</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">specifying</span> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">NSsites</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1314
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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">codeml</span><span class="p">,</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">example</span><span class="p">:</span> <span class="n" style="color: #333;">NSsites</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1315
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<pre style="margin: 0;">-<span id="LC1315" class="line" lang="mosel"> <span class="m" style="color: #099;">7</span> <span class="m" style="color: #099;">8.</span></span>
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1316
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<pre style="margin: 0;">-<span id="LC1316" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1317
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<pre style="margin: 0;">-<span id="LC1317" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">8</span><span class="p">)</span> <span class="n" style="color: #333;">baseml</span> <span class="p">&</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">ask</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">what</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">branch</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1318
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<pre style="margin: 0;">-<span id="LC1318" class="line" lang="mosel"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">fix_blength</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1319
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<pre style="margin: 0;">-<span id="LC1319" class="line" lang="mosel"> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">does</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">thing</span><span class="p">.</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1320
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<pre style="margin: 0;">-<span id="LC1320" class="line" lang="mosel"> <span class="n" style="color: #333;">fix_blength</span> <span class="p">=</span> <span class="p">-</span><span class="m" style="color: #099;">1</span> <span class="p">*</span> <span class="m" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">ignore</span><span class="p">,</span> <span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">random</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">initial</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">fixed</span></span>
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1321
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<pre style="margin: 0;">-<span id="LC1321" class="line" lang="mosel"></span>
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1322
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<pre style="margin: 0;">-<span id="LC1322" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1323
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<pre style="margin: 0;">-<span id="LC1323" class="line" lang="mosel"></span>
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1324
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<pre style="margin: 0;">-<span id="LC1324" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.12</span><span class="p">,</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">2002</span></span>
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1325
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<pre style="margin: 0;">-<span id="LC1325" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1326
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<pre style="margin: 0;">-<span id="LC1326" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span><span class="p">,</span> <span class="n" style="color: #333;">Mgene</span><span class="p">=</span><span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">4</span> <span class="p">(</span><span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">pi</span><span class="s1" style="color: #d14;">'s) and RateAncestor</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1327
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<pre style="margin: 0;">-<span id="LC1327" class="line" lang="mosel"><span class="s1" style="color: #d14;"> = 1 Ancestral reconstruction does not work properly although the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1328
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<pre style="margin: 0;">-<span id="LC1328" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ML iteration is fine. The output likelihood values (in the form</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1329
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<pre style="margin: 0;">-<span id="LC1329" class="line" lang="mosel"><span class="s1" style="color: #d14;"> "Node 20: lnL = -1047.965624") are different from the optimum</span></span>
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1330
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<pre style="margin: 0;">-<span id="LC1330" class="line" lang="mosel"><span class="s1" style="color: #d14;"> likelihood already calculated. The option was fine in version</span></span>
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1331
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<pre style="margin: 0;">-<span id="LC1331" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 3.0e and 3.1, and was broken in version 3.11.</span></span>
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1332
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<pre style="margin: 0;">-<span id="LC1332" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1333
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<pre style="margin: 0;">-<span id="LC1333" class="line" lang="mosel"><span class="s1" style="color: #d14;">(2) codeml stops with an error message "pi=0" when some amino acids are </span></span>
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1334
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<pre style="margin: 0;">-<span id="LC1334" class="line" lang="mosel"><span class="s1" style="color: #d14;"> missing in the sequences. Earlier versions of the program are correct.</span></span>
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1335
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<pre style="margin: 0;">-<span id="LC1335" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1336
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<pre style="margin: 0;">-<span id="LC1336" class="line" lang="mosel"><span class="s1" style="color: #d14;">(3) yn00 now accepts multiple data sets (specified by ndata).</span></span>
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1337
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<pre style="margin: 0;">-<span id="LC1337" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1338
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<pre style="margin: 0;">-<span id="LC1338" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1339
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<pre style="margin: 0;">-<span id="LC1339" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.11, September 2001</span></span>
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1340
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<pre style="margin: 0;">-<span id="LC1340" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1341
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<pre style="margin: 0;">-<span id="LC1341" class="line" lang="mosel"><span class="s1" style="color: #d14;">(1) baseml and codeml (clock = 1 or clock = 2) sometimes print out</span></span>
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1342
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<pre style="margin: 0;">-<span id="LC1342" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ridiculous (e.g., large negative) tree lengths and branch lengths.</span></span>
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1343
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<pre style="margin: 0;">-<span id="LC1343" class="line" lang="mosel"><span class="s1" style="color: #d14;"> I thought this was fixed in version 3.1, but it was not.</span></span>
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1344
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<pre style="margin: 0;">-<span id="LC1344" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Hopefully it is now fixed.</span></span>
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1345
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<pre style="margin: 0;">-<span id="LC1345" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1346
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<pre style="margin: 0;">-<span id="LC1346" class="line" lang="mosel"><span class="s1" style="color: #d14;">(2) baseml and codeml: Malpha (a separate alpha for each site</span></span>
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1347
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<pre style="margin: 0;">-<span id="LC1347" class="line" lang="mosel"><span class="s1" style="color: #d14;"> partition) does not work with Mgene = 0. The output will give you</span></span>
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1348
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<pre style="margin: 0;">-<span id="LC1348" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the same alpha value for each gene as you specify in the control</span></span>
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1349
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<pre style="margin: 0;">-<span id="LC1349" class="line" lang="mosel"><span class="s1" style="color: #d14;"> file. This is now fixed.</span></span>
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1350
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<pre style="margin: 0;">-<span id="LC1350" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1351
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<pre style="margin: 0;">-<span id="LC1351" class="line" lang="mosel"><span class="s1" style="color: #d14;">(3) baseml: When the REV or UNREST models (model = 6 or 7) are used</span></span>
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1352
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<pre style="margin: 0;">-<span id="LC1352" class="line" lang="mosel"><span class="s1" style="color: #d14;"> together with Mgene = 2, 3, 4, the program outputs one Q matrix,</span></span>
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1353
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<pre style="margin: 0;">-<span id="LC1353" class="line" lang="mosel"><span class="s1" style="color: #d14;"> when each site partition should have a different Q matrix. The ML</span></span>
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1354
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<pre style="margin: 0;">-<span id="LC1354" class="line" lang="mosel"><span class="s1" style="color: #d14;"> parameter estimates are correct, but I did not bother to format</span></span>
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1355
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<pre style="margin: 0;">-<span id="LC1355" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the output correctly. The single Q matrix in the output is the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1356
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<pre style="margin: 0;">-<span id="LC1356" class="line" lang="mosel"><span class="s1" style="color: #d14;"> one for the first partition. I have added the output for the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1357
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<pre style="margin: 0;">-<span id="LC1357" class="line" lang="mosel"><span class="s1" style="color: #d14;"> other matrices now.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1358
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<pre style="margin: 0;">-<span id="LC1358" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1359
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1359" class="line" lang="mosel"><span class="s1" style="color: #d14;">(4) baseml and codeml. Ancestral reconstruction was disabled for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1360
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<pre style="margin: 0;">-<span id="LC1360" class="line" lang="mosel"><span class="s1" style="color: #d14;"> large trees with more than 100 or 200 sequences in previous</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1361
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1361" class="line" lang="mosel"><span class="s1" style="color: #d14;"> versions. It is now allowed. On large trees, the multiplication</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1362
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1362" class="line" lang="mosel"><span class="s1" style="color: #d14;"> of transition probabilities across branches in the tree cause the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1363
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<pre style="margin: 0;">-<span id="LC1363" class="line" lang="mosel"><span class="s1" style="color: #d14;"> product to become too small to be represented in the computer.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1364
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<pre style="margin: 0;">-<span id="LC1364" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This is known as underflows. I implemented a scaling algorithm to</span></span>
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1365
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<pre style="margin: 0;">-<span id="LC1365" class="line" lang="mosel"><span class="s1" style="color: #d14;"> avoid underflows some time ago but did not bother to do it with</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1366
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<pre style="margin: 0;">-<span id="LC1366" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the ancestral reconstruction algorithm at the time. The algorithm</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1367
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<pre style="margin: 0;">-<span id="LC1367" class="line" lang="mosel"><span class="s1" style="color: #d14;"> should now work, up to the upper limit set in the program, that</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1368
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<pre style="margin: 0;">-<span id="LC1368" class="line" lang="mosel"><span class="s1" style="color: #d14;"> is, 1000 or 2000 sequences.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1369
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<pre style="margin: 0;">-<span id="LC1369" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1370
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<pre style="margin: 0;">-<span id="LC1370" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1371
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<pre style="margin: 0;">-<span id="LC1371" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1372
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1372" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.1, June 2001</span></span>
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1373
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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1374
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1374" class="line" lang="mosel"><span class="s1" style="color: #d14;">Changed the way of counting base or amino acid frequencies so that</span></span>
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1375
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="mosel"><span class="s1" style="color: #d14;">this version of baseml or codeml might generate different results from</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1376
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<pre style="margin: 0;">-<span id="LC1376" class="line" lang="mosel"><span class="s1" style="color: #d14;">previous versions under the following model specifications. </span></span>
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1377
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<pre style="margin: 0;">-<span id="LC1377" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1378
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<pre style="margin: 0;">-<span id="LC1378" class="line" lang="mosel"><span class="s1" style="color: #d14;"> . baseml & aaml: if you have multiple genes and the model uses the same</span></span>
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1379
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<pre style="margin: 0;">-<span id="LC1379" class="line" lang="mosel"><span class="s1" style="color: #d14;"> frequencies in the model for the different site partitions. </span></span>
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1380
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<pre style="margin: 0;">-<span id="LC1380" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1381
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<pre style="margin: 0;">-<span id="LC1381" class="line" lang="mosel"><span class="s1" style="color: #d14;"> . codonml:</span></span>
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1382
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<pre style="margin: 0;">-<span id="LC1382" class="line" lang="mosel"><span class="s1" style="color: #d14;"> if you have ambiguity characters at all. Ambiguity characters were</span></span>
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1383
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<pre style="margin: 0;">-<span id="LC1383" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ignored when counting frequencies in previous versions but are used now.</span></span>
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1384
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<pre style="margin: 0;">-<span id="LC1384" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1385
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<pre style="margin: 0;">-<span id="LC1385" class="line" lang="mosel"><span class="s1" style="color: #d14;">There is no difference if your data do not contain any alignment gaps</span></span>
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1386
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<pre style="margin: 0;">-<span id="LC1386" class="line" lang="mosel"><span class="s1" style="color: #d14;">or ambiguity characters or if you choose to remove them before any</span></span>
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1387
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<pre style="margin: 0;">-<span id="LC1387" class="line" lang="mosel"><span class="s1" style="color: #d14;">analysis (cleandata = 1). The early versions used two ad hoc methods</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1388
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<pre style="margin: 0;">-<span id="LC1388" class="line" lang="mosel"><span class="s1" style="color: #d14;">in dealing with such ambiguity characters in different places of the</span></span>
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1389
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<pre style="margin: 0;">-<span id="LC1389" class="line" lang="mosel"><span class="s1" style="color: #d14;">programs. The new version uses another ad hoc method and in all</span></span>
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1390
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<pre style="margin: 0;">-<span id="LC1390" class="line" lang="mosel"><span class="s1" style="color: #d14;">places. I think it will be fine which ever version you use, but do</span></span>
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1391
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<pre style="margin: 0;">-<span id="LC1391" class="line" lang="mosel"><span class="s1" style="color: #d14;">not use different versions in the same analysis.</span></span>
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1392
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<pre style="margin: 0;">-<span id="LC1392" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1393
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<pre style="margin: 0;">-<span id="LC1393" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml with seqtype = 1) with Mgene = 1 does not work</span></span>
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1394
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<pre style="margin: 0;">-<span id="LC1394" class="line" lang="mosel"><span class="s1" style="color: #d14;">correctly if the sequences have alignment gaps or ambiguity</span></span>
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1395
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<pre style="margin: 0;">-<span id="LC1395" class="line" lang="mosel"><span class="s1" style="color: #d14;">characters. Mgene = 1 means separate analysis. The bug causes data</span></span>
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1396
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<pre style="margin: 0;">-<span id="LC1396" class="line" lang="mosel"><span class="s1" style="color: #d14;">for the genes except the first to be read out of frames, so that most</span></span>
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1397
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="mosel"><span class="s1" style="color: #d14;">likely you will see a lot of messages "stop codon XXX" before the</span></span>
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1398
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<pre style="margin: 0;">-<span id="LC1398" class="line" lang="mosel"><span class="s1" style="color: #d14;">program aborts. This is now fixed.</span></span>
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1399
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<pre style="margin: 0;">-<span id="LC1399" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1400
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml with seqtype = 1) with fix_alpha=0: In the final</span></span>
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1402
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="mosel"><span class="s1" style="color: #d14;">output for the codon + gamma model, parameter alpha is not correctly</span></span>
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1403
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="mosel"><span class="s1" style="color: #d14;">identified. If you have fix_kappa = 0, fix_omega =0, and fix_alpha=0,</span></span>
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1404
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<pre style="margin: 0;">-<span id="LC1404" class="line" lang="mosel"><span class="s1" style="color: #d14;">the last three numbers should be kappa, omega (dn/ds), and alpha. The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1405
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<pre style="margin: 0;">-<span id="LC1405" class="line" lang="mosel"><span class="s1" style="color: #d14;">detailed output did not identify alpha correctly, although the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1406
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="mosel"><span class="s1" style="color: #d14;">likelihood value and the outputted rates and frequencies (r and f) are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1407
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="mosel"><span class="s1" style="color: #d14;">correct. I believe this is now corrected.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1408
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1409
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<pre style="margin: 0;">-<span id="LC1409" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1410
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1411
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 3.0e, 14 May 2001</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1412
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<pre style="margin: 0;">-<span id="LC1412" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1413
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<pre style="margin: 0;">-<span id="LC1413" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml with seqtype = 1) with model = 1: The program crashes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1414
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="mosel"><span class="s1" style="color: #d14;">when you have a small tree with <= 5 branches. This is a new error</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1415
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="mosel"><span class="s1" style="color: #d14;">introduced in version 3.0c. It is now fixed.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1416
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1417
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<pre style="margin: 0;">-<span id="LC1417" class="line" lang="mosel"><span class="s1" style="color: #d14;">baseml and codeml (clock = 1 or clock = 2) sometimes print out ridiculous</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1418
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<pre style="margin: 0;">-<span id="LC1418" class="line" lang="mosel"><span class="s1" style="color: #d14;">tree lengths and branch lengths. </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1419
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<pre style="margin: 0;">-<span id="LC1419" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1420
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<pre style="margin: 0;">-<span id="LC1420" class="line" lang="mosel"><span class="s1" style="color: #d14;">yn00 in version 3.0c ignores icode and uses the universal code only.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1421
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="mosel"><span class="s1" style="color: #d14;">It was correct in vesion 3.0b. This is fixed in version 3.0d.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1422
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1423
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<pre style="margin: 0;">-<span id="LC1423" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1424
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1424" class="line" lang="mosel"><span class="s1" style="color: #d14;">Versions 3.0c-3.0d, 20 February 2001</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1425
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<pre style="margin: 0;">-<span id="LC1425" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1426
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<pre style="margin: 0;">-<span id="LC1426" class="line" lang="mosel"><span class="s1" style="color: #d14;">We bought a Pentium III cluster running redhat linux 6.2. The gcc</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1427
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<pre style="margin: 0;">-<span id="LC1427" class="line" lang="mosel"><span class="s1" style="color: #d14;">compiler 2.61 seems to have bugs and codeml does not run for NSsites =</span></span>
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1428
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<pre style="margin: 0;">-<span id="LC1428" class="line" lang="mosel"><span class="s1" style="color: #d14;">7 or 8. The program might output "points out of order" or "Det goes</span></span>
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1429
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<pre style="margin: 0;">-<span id="LC1429" class="line" lang="mosel"><span class="s1" style="color: #d14;">to 0" error messages. 3.0d seems to be safer for these models.</span></span>
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1430
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<pre style="margin: 0;">-<span id="LC1430" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1431
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<pre style="margin: 0;">-<span id="LC1431" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml with seqtype = 1) with NSsites = 3 might generate a</span></span>
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1432
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<pre style="margin: 0;">-<span id="LC1432" class="line" lang="mosel"><span class="s1" style="color: #d14;">message "error: sortwM3." and then stop with no output after the</span></span>
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1433
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<pre style="margin: 0;">-<span id="LC1433" class="line" lang="mosel"><span class="s1" style="color: #d14;">iteration. This is now fixed. During the iteration, there was no</span></span>
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1434
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<pre style="margin: 0;">-<span id="LC1434" class="line" lang="mosel"><span class="s1" style="color: #d14;">restriction on the w values, so that w0 can be greater than w1 and so</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1435
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<pre style="margin: 0;">-<span id="LC1435" class="line" lang="mosel"><span class="s1" style="color: #d14;">on. At the end of the iteration, I sort the three w values so that w0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1436
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<pre style="margin: 0;">-<span id="LC1436" class="line" lang="mosel"><span class="s1" style="color: #d14;">< w1 < w2 before outputting. 3.0c has a bug at sorting. If you don'</span><span class="n" style="color: #333;">t</span></span>
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1437
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<pre style="margin: 0;">-<span id="LC1437" class="line" lang="mosel"><span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">everything</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fine</span><span class="p">.</span></span>
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1438
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<pre style="margin: 0;">-<span id="LC1438" class="line" lang="mosel"></span>
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1439
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<pre style="margin: 0;">-<span id="LC1439" class="line" lang="mosel"></span>
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1440
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<pre style="margin: 0;">-<span id="LC1440" class="line" lang="mosel"><span class="m" style="color: #099;">10</span> <span class="n" style="color: #333;">November</span> <span class="m" style="color: #099;">2000</span></span>
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1441
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<pre style="margin: 0;">-<span id="LC1441" class="line" lang="mosel"></span>
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1442
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<pre style="margin: 0;">-<span id="LC1442" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">probabilities</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Joint</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">correct</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1443
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<pre style="margin: 0;">-<span id="LC1443" class="line" lang="mosel"><span class="n" style="color: #333;">Many</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">larger</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">Fixed</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">3.0</span><span class="n" style="color: #333;">c</span><span class="p">.</span></span>
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1444
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<pre style="margin: 0;">-<span id="LC1444" class="line" lang="mosel"></span>
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1445
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<pre style="margin: 0;">-<span id="LC1445" class="line" lang="mosel"></span>
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1446
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<pre style="margin: 0;">-<span id="LC1446" class="line" lang="mosel"></span>
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1447
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<pre style="margin: 0;">-<span id="LC1447" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.0</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="m" style="color: #099;">30</span> <span class="n" style="color: #333;">October</span> <span class="m" style="color: #099;">2000</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1448
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<pre style="margin: 0;">-<span id="LC1448" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1449
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1449" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">Changed</span> <span class="n" style="color: #333;">parameterization</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">3</span><span class="p">),</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span></span>
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1450
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<pre style="margin: 0;">-<span id="LC1450" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">lists</span> <span class="n" style="color: #333;">node</span> <span class="n" style="color: #333;">ages</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">SEs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">node</span> <span class="n" style="color: #333;">ages</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1451
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1451" class="line" lang="mosel"><span class="n" style="color: #333;">Node</span> <span class="n" style="color: #333;">ages</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">measured</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">expected</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">nucleotide</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">amino</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1452
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1452" class="line" lang="mosel"><span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">substitutions</span> <span class="n" style="color: #333;">per</span> <span class="n" style="color: #333;">site</span> <span class="p">(</span><span class="n" style="color: #333;">nucleotide</span><span class="p">,</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">codon</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1453
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1453" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">node</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">present</span> <span class="n" style="color: #333;">time</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">proportional</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">divergence</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1454
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1454" class="line" lang="mosel"><span class="n" style="color: #333;">times</span><span class="p">.</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">versions</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">proportions</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1455
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1455" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1456
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1456" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">codonml</span><span class="p">:</span> <span class="n" style="color: #333;">problem</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NSsites</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">gene</span> <span class="n" style="color: #333;">data</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1457
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1457" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">Mgene</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">(?).</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">earlier</span> <span class="k" style="font-weight: 600;">version</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">likelihood</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1458
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1458" class="line" lang="mosel"><span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">.,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">identification</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sites</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">positive</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1459
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1459" class="line" lang="mosel"><span class="n" style="color: #333;">selection</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">incorrect</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">attempted</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1460
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1460" class="line" lang="mosel"><span class="n" style="color: #333;">another</span> <span class="n" style="color: #333;">gene</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">analyzing</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">Mgene</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1461
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1461" class="line" lang="mosel"><span class="k" style="font-weight: 600;">options</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">codons</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acids</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1462
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1462" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1463
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1463" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1464
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1464" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1465
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1465" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3.0</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="m" style="color: #099;">6</span> <span class="n" style="color: #333;">October</span> <span class="m" style="color: #099;">2000</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1466
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1466" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1467
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1467" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">correctly</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">paml3</span><span class="m" style="color: #099;">.0</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">3.0</span><span class="n" style="color: #333;">a</span><span class="p">.</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1468
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<pre style="margin: 0;">-<span id="LC1468" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1469
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1469" class="line" lang="mosel"><span class="n" style="color: #333;">Yoder</span><span class="p">,</span> <span class="n" style="color: #333;">A</span><span class="p">.</span> <span class="n" style="color: #333;">D</span><span class="p">.,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Z</span><span class="p">.</span> <span class="n" style="color: #333;">Yang</span><span class="p">.</span> <span class="m" style="color: #099;">2000.</span> <span class="n" style="color: #333;">Estimation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">primate</span> <span class="n" style="color: #333;">speciation</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1470
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<pre style="margin: 0;">-<span id="LC1470" class="line" lang="mosel"><span class="n" style="color: #333;">dates</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">molecular</span> <span class="n" style="color: #333;">clocks</span><span class="p">.</span> <span class="n" style="color: #333;">Molecular</span> <span class="n" style="color: #333;">Biology</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Evolution</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1471
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1471" class="line" lang="mosel"><span class="m" style="color: #099;">17</span> <span class="p">(</span><span class="m" style="color: #099;">7</span><span class="p">):</span> <span class="m" style="color: #099;">1081</span><span class="p">-</span><span class="m" style="color: #099;">1090.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1472
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1472" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1473
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1473" class="line" lang="mosel"><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">serious</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">made</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">available</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1474
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1474" class="line" lang="mosel"><span class="k" style="font-weight: 600;">public</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ver3</span><span class="m" style="color: #099;">.0</span> <span class="p">(</span><span class="n" style="color: #333;">May</span> <span class="m" style="color: #099;">2000</span><span class="p">).</span> <span class="n" style="color: #333;">Two</span> <span class="n" style="color: #333;">symptoms</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">noted</span> <span class="n" style="color: #333;">right</span> <span class="n" style="color: #333;">now</span><span class="p">:</span> <span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1475
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1475" class="line" lang="mosel"><span class="n" style="color: #333;">crashes</span> <span class="p">(</span><span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">good</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">make</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">realise</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">something</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1476
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1476" class="line" lang="mosel"><span class="n" style="color: #333;">wrong</span> <span class="n" style="color: #333;">immediately</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">(</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span><span class="p">=</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">having</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1477
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1477" class="line" lang="mosel"><span class="n" style="color: #333;">worse</span> <span class="n" style="color: #333;">likelihood</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">global</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">(</span><span class="n" style="color: #333;">clock</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">results</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1478
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1478" class="line" lang="mosel"><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">paper</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">typo</span> <span class="p">(</span><span class="s2" style="color: #d14;">"37.30 - 48.48"</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span> <span class="m" style="color: #099;">3</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1479
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1479" class="line" lang="mosel"><span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">cetacean</span><span class="p">-</span><span class="n" style="color: #333;">whale</span> <span class="n" style="color: #333;">divergence</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">C3</span> <span class="n" style="color: #333;">calibration</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1480
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1480" class="line" lang="mosel"><span class="s2" style="color: #d14;">"57.30 - 48.48"</span><span class="p">).</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">now</span> <span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">results</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1481
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1481" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">paper</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">help</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">prepare</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">own</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">files</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1482
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1482" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1483
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1483" class="line" lang="mosel"><span class="n" style="color: #333;">Sorry</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">damages</span> <span class="n" style="color: #333;">done</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1484
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1484" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1485
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1485" class="line" lang="mosel"><span class="n" style="color: #333;">Many</span> <span class="n" style="color: #333;">thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Toby</span> <span class="n" style="color: #333;">Johnson</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Philip</span> <span class="n" style="color: #333;">Awadalla</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">spotting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">error</span><span class="p">.</span></span>
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1486
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<pre style="margin: 0;">-<span id="LC1486" class="line" lang="mosel"></span>
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1487
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<pre style="margin: 0;">-<span id="LC1487" class="line" lang="mosel"></span>
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1488
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<pre style="margin: 0;">-<span id="LC1488" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1489
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<pre style="margin: 0;">-<span id="LC1489" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">3</span><span class="p">,</span> <span class="m" style="color: #099;">4</span> <span class="n" style="color: #333;">February</span> <span class="m" style="color: #099;">2000</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1490
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<pre style="margin: 0;">-<span id="LC1490" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1491
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1491" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">evolver</span> <span class="n" style="color: #333;">may</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">correctly</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">branch</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1492
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1492" class="line" lang="mosel"><span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">large</span><span class="p">,</span> <span class="n" style="color: #333;">say</span> <span class="p">></span><span class="m" style="color: #099;">10.</span> </span>
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1493
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<pre style="margin: 0;">-<span id="LC1493" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1494
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1494" class="line" lang="mosel"><span class="n" style="color: #333;">Scaling</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">nodes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">underflow</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1495
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1495" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="p">(</span><span class="n" style="color: #333;">say</span> <span class="p">></span> <span class="m" style="color: #099;">200</span> <span class="k" style="font-weight: 600;">or</span> <span class="m" style="color: #099;">300</span><span class="p">),</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">probability</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">observing</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1496
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1496" class="line" lang="mosel"><span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">too</span> <span class="n" style="color: #333;">small</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">represent</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">machine</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1497
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1497" class="line" lang="mosel"><span class="n" style="color: #333;">because</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">probabilities</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">multiplied</span> <span class="n" style="color: #333;">along</span> <span class="n" style="color: #333;">branches</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1498
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1498" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">branches</span><span class="p">.</span> <span class="n" style="color: #333;">Since</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">2.0</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">underflow</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1499
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1499" class="line" lang="mosel"><span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">dealt</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">scaling</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">works</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">one</span><span class="p">-</span><span class="n" style="color: #333;">rate</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1500
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1500" class="line" lang="mosel"><span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">did</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">NSsites</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1501
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1501" class="line" lang="mosel"><span class="n" style="color: #333;">codonml</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">probably</span> <span class="n" style="color: #333;">nobody</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">analysed</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">notice</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1502
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1502" class="line" lang="mosel"><span class="n" style="color: #333;">this</span><span class="p">.</span> <span class="n" style="color: #333;">Anyway</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">version</span> <span class="n" style="color: #333;">hopefully</span> <span class="n" style="color: #333;">fixes</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">problem</span><span class="p">,</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">was</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1503
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1503" class="line" lang="mosel"><span class="n" style="color: #333;">analysing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">set</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Bush</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">1999</span> <span class="n" style="color: #333;">MBE</span> <span class="m" style="color: #099;">16</span><span class="p">:</span><span class="m" style="color: #099;">1457</span><span class="p">-</span><span class="m" style="color: #099;">1465</span><span class="p">),</span> <span class="n" style="color: #333;">which</span></span>
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1504
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<pre style="margin: 0;">-<span id="LC1504" class="line" lang="mosel"><span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">about</span> <span class="m" style="color: #099;">350</span> <span class="n" style="color: #333;">sequences</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">data</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1505
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1505" class="line" lang="mosel"><span class="n" style="color: #333;">sets</span><span class="p">,</span> <span class="n" style="color: #333;">watch</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">anything</span> <span class="n" style="color: #333;">strange</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">let</span> <span class="n" style="color: #333;">me</span> <span class="n" style="color: #333;">know</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">suppose</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1506
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1506" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">supplied</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">such</span> <span class="n" style="color: #333;">sizes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1507
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1507" class="line" lang="mosel"><span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">manageable</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">scaling</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">important</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1508
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1508" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1509
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1509" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1510
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1510" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1511
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1511" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">Oct</span> <span class="m" style="color: #099;">14</span><span class="p">,</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1512
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1512" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1513
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1513" class="line" lang="mosel"><span class="n" style="color: #333;">Fixed</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">errors</span><span class="p">,</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">simple</span> <span class="n" style="color: #333;">errors</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1514
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1514" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1515
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1515" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">RemoveIndel</span> <span class="n" style="color: #333;">routine</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">e</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">20.f</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">removes</span> <span class="n" style="color: #333;">most</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1516
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1516" class="line" lang="mosel"><span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">those</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">T</span><span class="s1" style="color: #d14;">'s and C'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">baseml</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1517
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1517" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">routine</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">g</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">removes</span> <span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">sites</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1518
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1518" class="line" lang="mosel"><span class="n" style="color: #333;">except</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">T</span><span class="s1" style="color: #d14;">'s and C'</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">aaml</span><span class="p">.</span> <span class="k" style="font-weight: 600;">In</span> <span class="n" style="color: #333;">either</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1519
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1519" class="line" lang="mosel"><span class="k" style="font-weight: 600;">case</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">grossly</span> <span class="n" style="color: #333;">wrong</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bugs</span> <span class="n" style="color: #333;">affect</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">analysis</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1520
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1520" class="line" lang="mosel"><span class="n" style="color: #333;">only</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">gaps</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ambiguity</span> <span class="n" style="color: #333;">characters</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">use</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1521
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<pre style="margin: 0;">-<span id="LC1521" class="line" lang="mosel"><span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">aaml</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">e</span> <span class="k" style="font-weight: 600;">and</span> <span class="m" style="color: #099;">2.0f</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">codonml</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1522
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<pre style="margin: 0;">-<span id="LC1522" class="line" lang="mosel"><span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">g</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1523
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1523" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1524
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1524" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">newly</span> <span class="n" style="color: #333;">introduced</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">baseml</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1525
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1525" class="line" lang="mosel"><span class="p">(</span><span class="n" style="color: #333;">icode</span><span class="p">)</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">aborts</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">message</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1526
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1526" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1527
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1527" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1528
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1528" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1529
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1529" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1530
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<pre style="margin: 0;">-<span id="LC1530" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1531
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1531" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">Sept</span> <span class="m" style="color: #099;">21</span><span class="p">,</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1532
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1532" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1533
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1533" class="line" lang="mosel"><span class="n" style="color: #333;">Fixed</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">2.0f</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">causes</span> <span class="n" style="color: #333;">crash</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">getSE</span> <span class="p">=</span> <span class="m" style="color: #099;">1.</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1534
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1534" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1535
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1535" class="line" lang="mosel"><span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">codeml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">in</span> <span class="m" style="color: #099;">2.0f</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">simply</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1536
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1536" class="line" lang="mosel"><span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">estimating</span> <span class="n" style="color: #333;">them</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">iteration</span><span class="p">.</span> <span class="n" style="color: #333;">I</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1537
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1537" class="line" lang="mosel"><span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">question</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">choose</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">ignore</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1538
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1538" class="line" lang="mosel"><span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">initial</span> <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1539
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1539" class="line" lang="mosel"><span class="n" style="color: #333;">iteration</span><span class="p">.</span></span>
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1540
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1540" class="line" lang="mosel"></span>
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1541
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<pre style="margin: 0;">-<span id="LC1541" class="line" lang="mosel"></span>
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1542
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<pre style="margin: 0;">-<span id="LC1542" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1543
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1543" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">June</span> <span class="m" style="color: #099;">30</span><span class="p">,</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1544
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1544" class="line" lang="mosel"><span class="n" style="color: #333;">Fixed</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">convergence</span> <span class="n" style="color: #333;">problems</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ML</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">estimation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">dS</span> <span class="k" style="font-weight: 600;">and</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1545
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1545" class="line" lang="mosel"><span class="n" style="color: #333;">dN</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">particular</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">presence</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">partitions</span> <span class="p">(</span><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">G</span> <span class="n" style="color: #333;">option</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1546
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<pre style="margin: 0;">-<span id="LC1546" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1547
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1547" class="line" lang="mosel"><span class="n" style="color: #333;">Fixed</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">evolver</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">sensible</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1548
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1548" class="line" lang="mosel"><span class="n" style="color: #333;">generated</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">smaller</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">1e-7</span><span class="p">.</span> <span class="n" style="color: #333;">At</span> <span class="n" style="color: #333;">some</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1549
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1549" class="line" lang="mosel"><span class="n" style="color: #333;">point</span><span class="p">,</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">did</span> <span class="n" style="color: #333;">something</span> <span class="s2" style="color: #d14;">"clever"</span> <span class="p">(</span><span class="n" style="color: #333;">taking</span> <span class="n" style="color: #333;">advantage</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">fact</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">at</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1550
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1550" class="line" lang="mosel"><span class="n" style="color: #333;">such</span> <span class="n" style="color: #333;">small</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">evolution</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">occur</span><span class="p">),</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">destroyed</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1551
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1551" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">calculation</span><span class="p">.</span> </span>
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1552
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<pre style="margin: 0;">-<span id="LC1552" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1553
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1553" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1554
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1554" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1555
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1555" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">2.0</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">May</span> <span class="m" style="color: #099;">12</span><span class="p">,</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1556
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1556" class="line" lang="mosel"><span class="n" style="color: #333;">Corrected</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">problems</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">evolver</span> <span class="n" style="color: #333;">program</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">running</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1557
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1557" class="line" lang="mosel"><span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">baseml</span><span class="p">.</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">REV</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">MCbase</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1558
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1558" class="line" lang="mosel"><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">John</span> <span class="n" style="color: #333;">Mercer</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1559
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1559" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1560
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1560" class="line" lang="mosel"><span class="n" style="color: #333;">Note</span><span class="p">--</span><span class="n" style="color: #333;">Uncomment</span> <span class="n" style="color: #333;">ndata</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">codeml</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">analyse</span> <span class="n" style="color: #333;">multiple</span></span>
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1561
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<pre style="margin: 0;">-<span id="LC1561" class="line" lang="mosel"><span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span> <span class="n" style="color: #333;">generated</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">evolver</span><span class="p">.</span></span>
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1562
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<pre style="margin: 0;">-<span id="LC1562" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1563
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<pre style="margin: 0;">-<span id="LC1563" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1564
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1564" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1565
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1565" class="line" lang="mosel"><span class="n" style="color: #333;">April</span> <span class="m" style="color: #099;">16</span><span class="p">,</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1566
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1566" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1567
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1567" class="line" lang="mosel"><span class="n" style="color: #333;">Although</span> <span class="n" style="color: #333;">posted</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">days</span> <span class="n" style="color: #333;">ago</span><span class="p">,</span> <span class="n" style="color: #333;">paml2</span><span class="m" style="color: #099;">.0</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">error</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1568
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1568" class="line" lang="mosel"><span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">codeml</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">invalidates</span> <span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">analyses</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">codon</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1569
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1569" class="line" lang="mosel"><span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">models</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">symptom</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">relatively</span> <span class="n" style="color: #333;">easy</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">spot</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1570
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1570" class="line" lang="mosel"><span class="n" style="color: #333;">indicated</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">parameters</span> <span class="p">(</span><span class="n" style="color: #333;">say</span> <span class="n" style="color: #333;">omega</span><span class="p">)</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">being</span> <span class="n" style="color: #333;">estimated</span> <span class="n" style="color: #333;">at</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1571
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1571" class="line" lang="mosel"><span class="n" style="color: #333;">all</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">exactly</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">you</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1572
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1572" class="line" lang="mosel"><span class="n" style="color: #333;">specified</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1573
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<pre style="margin: 0;">-<span id="LC1573" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1574
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1574" class="line" lang="mosel"><span class="n" style="color: #333;">Amino</span> <span class="n" style="color: #333;">acid</span><span class="p">-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">analysis</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">comparison</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">sequences</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1575
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1575" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">affected</span><span class="p">.</span> <span class="n" style="color: #333;">Use</span> <span class="n" style="color: #333;">paml2</span><span class="m" style="color: #099;">.0</span><span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">redo</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">analysis</span><span class="p">.</span> <span class="n" style="color: #333;">Apologies</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1576
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1576" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">trouble</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1577
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1577" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1578
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1578" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1579
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1579" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1580
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1580" class="line" lang="mosel"><span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">2.0</span><span class="p">,</span> <span class="m" style="color: #099;">31</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1581
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<pre style="margin: 0;">-<span id="LC1581" class="line" lang="mosel"><span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">back</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">faster</span> <span class="n" style="color: #333;">calculation</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">data</span><span class="p">.</span></span>
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1582
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<pre style="margin: 0;">-<span id="LC1582" class="line" lang="mosel"><span class="n" style="color: #333;">Enabled</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">programs</span><span class="p">/</span><span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">broke</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">temporary</span> <span class="n" style="color: #333;">versions</span><span class="p">,</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1583
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<pre style="margin: 0;">-<span id="LC1583" class="line" lang="mosel"><span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pamp</span><span class="p">,</span> <span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">reconstruction</span><span class="p">.</span></span>
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1584
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<pre style="margin: 0;">-<span id="LC1584" class="line" lang="mosel"></span>
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1585
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1585" class="line" lang="mosel"><span class="n" style="color: #333;">Renamed</span> <span class="n" style="color: #333;">listtree</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">evolver</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">simulation</span> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span></span>
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1586
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<pre style="margin: 0;">-<span id="LC1586" class="line" lang="mosel"></span>
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1587
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<pre style="margin: 0;">-<span id="LC1587" class="line" lang="mosel"></span>
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1588
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<pre style="margin: 0;">-<span id="LC1588" class="line" lang="mosel"></span>
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1589
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<pre style="margin: 0;">-<span id="LC1589" class="line" lang="mosel"><span class="n" style="color: #333;">PAML</span> <span class="m" style="color: #099;">1.4</span> <span class="n" style="color: #333;">Temporary</span> <span class="n" style="color: #333;">versions</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1590
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<pre style="margin: 0;">-<span id="LC1590" class="line" lang="mosel"><span class="n" style="color: #333;">Dec98</span> <span class="p">&</span> <span class="n" style="color: #333;">Jan99</span> </span>
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1591
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<pre style="margin: 0;">-<span id="LC1591" class="line" lang="mosel"></span>
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1592
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<pre style="margin: 0;">-<span id="LC1592" class="line" lang="mosel"> <span class="n" style="color: #333;">pamlTMP</span><span class="p">.</span><span class="n" style="color: #333;">Jan99</span><span class="p">.</span><span class="n" style="color: #333;">notes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1593
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<pre style="margin: 0;">-<span id="LC1593" class="line" lang="mosel"> <span class="p">===================</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1594
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<pre style="margin: 0;">-<span id="LC1594" class="line" lang="mosel"> <span class="n" style="color: #333;">Ziheng</span> <span class="n" style="color: #333;">Yang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1595
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<pre style="margin: 0;">-<span id="LC1595" class="line" lang="mosel"> <span class="n" style="color: #333;">Fri</span> <span class="n" style="color: #333;">Jan</span> <span class="m" style="color: #099;">15</span> <span class="m" style="color: #099;">10</span><span class="p">:</span><span class="m" style="color: #099;">01</span><span class="p">:</span><span class="m" style="color: #099;">42</span> <span class="n" style="color: #333;">GMT</span> <span class="m" style="color: #099;">1999</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1596
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<pre style="margin: 0;">-<span id="LC1596" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1597
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1597" class="line" lang="mosel"> <span class="p">.</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">make</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">compile</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">programs</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">got</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">messages</span><span class="p">,</span> <span class="n" style="color: #333;">see</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1598
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<pre style="margin: 0;">-<span id="LC1598" class="line" lang="mosel"> <span class="n" style="color: #333;">whether</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">know</span> <span class="n" style="color: #333;">how</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">Makefile</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1599
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<pre style="margin: 0;">-<span id="LC1599" class="line" lang="mosel"> <span class="n" style="color: #333;">either</span><span class="p">,</span> <span class="n" style="color: #333;">look</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">paml</span><span class="p">.</span><span class="n" style="color: #333;">cc</span><span class="p">,</span> <span class="n" style="color: #333;">paml</span><span class="p">.</span><span class="n" style="color: #333;">gcc</span><span class="p">,</span> <span class="n" style="color: #333;">etc</span><span class="p">.</span></span>
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1600
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<pre style="margin: 0;">-<span id="LC1600" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1601
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<pre style="margin: 0;">-<span id="LC1601" class="line" lang="mosel"> <span class="p">.</span><span class="n" style="color: #333;">At</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">suggestion</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">David</span> <span class="n" style="color: #333;">Posada</span><span class="p">,</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">ML</span> <span class="n" style="color: #333;">estimation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">pairwise</span> </span>
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1602
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<pre style="margin: 0;">-<span id="LC1602" class="line" lang="mosel"> <span class="n" style="color: #333;">distances</span> <span class="n" style="color: #333;">between</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> </span>
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1603
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<pre style="margin: 0;">-<span id="LC1603" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1604
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<pre style="margin: 0;">-<span id="LC1604" class="line" lang="mosel"> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">relavant</span> <span class="n" style="color: #333;">variables</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span> <span class="n" style="color: #333;">are</span> </span>
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1605
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<pre style="margin: 0;">-<span id="LC1605" class="line" lang="mosel"></span>
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1606
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<pre style="margin: 0;">-<span id="LC1606" class="line" lang="mosel"> <span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="p">-</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">calculation</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1607
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<pre style="margin: 0;">-<span id="LC1607" class="line" lang="mosel"> <span class="n" style="color: #333;">aaRatefile</span> <span class="p">=</span> <span class="n" style="color: #333;">jones</span><span class="p">.</span><span class="n" style="color: #333;">dat</span> <span class="p">*</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">aa</span> <span class="n" style="color: #333;">seqs</span> <span class="k" style="font-weight: 600;">with</span> <span class="k" style="font-weight: 600;">model</span><span class="p">=</span><span class="n" style="color: #333;">empirical</span><span class="p">(</span><span class="n" style="color: #333;">_F</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1608
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<pre style="margin: 0;">-<span id="LC1608" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">dayhoff</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span> <span class="n" style="color: #333;">jones</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span> <span class="n" style="color: #333;">mtmam</span><span class="p">.</span><span class="n" style="color: #333;">dat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">own</span></span>
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1609
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<pre style="margin: 0;">-<span id="LC1609" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">3</span> </span>
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1610
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<pre style="margin: 0;">-<span id="LC1610" class="line" lang="mosel"> <span class="n" style="color: #333;">alpha</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span></span>
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1611
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<pre style="margin: 0;">-<span id="LC1611" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1612
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<pre style="margin: 0;">-<span id="LC1612" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">specifies</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">substitution</span> <span class="k" style="font-weight: 600;">model</span><span class="p">.</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">choose</span></span>
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1613
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<pre style="margin: 0;">-<span id="LC1613" class="line" lang="mosel"> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">from</span> <span class="m" style="color: #099;">0</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="m" style="color: #099;">3.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">want</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">estimate</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">from</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1614
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<pre style="margin: 0;">-<span id="LC1614" class="line" lang="mosel"> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">should</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">move</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1615
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<pre style="margin: 0;">-<span id="LC1615" class="line" lang="mosel"> <span class="n" style="color: #333;">estimated</span> <span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">matrix</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">mlc</span><span class="p">)</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">a</span></span>
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1616
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<pre style="margin: 0;">-<span id="LC1616" class="line" lang="mosel"> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">aaRatefile</span><span class="p">.</span> </span>
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1617
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<pre style="margin: 0;">-<span id="LC1617" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1618
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<pre style="margin: 0;">-<span id="LC1618" class="line" lang="mosel"> <span class="n" style="color: #333;">Choosing</span> <span class="n" style="color: #333;">alpha</span><span class="p">></span><span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">distance</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">alpha</span></span>
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1619
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<pre style="margin: 0;">-<span id="LC1619" class="line" lang="mosel"> <span class="n" style="color: #333;">parameter</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">anything</span> <span class="n" style="color: #333;">strange</span><span class="p">,</span> <span class="n" style="color: #333;">please</span> <span class="n" style="color: #333;">let</span> <span class="n" style="color: #333;">me</span> <span class="n" style="color: #333;">know</span><span class="p">.</span></span>
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1620
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<pre style="margin: 0;">-<span id="LC1620" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1621
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<pre style="margin: 0;">-<span id="LC1621" class="line" lang="mosel"> <span class="p">.</span><span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">included</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">baseml</span><span class="p">,</span> <span class="n" style="color: #333;">codeml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">listtree</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1622
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<pre style="margin: 0;">-<span id="LC1622" class="line" lang="mosel"> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">others</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">they</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">included</span><span class="p">.</span></span>
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1623
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<pre style="margin: 0;">-<span id="LC1623" class="line" lang="mosel"></span>
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1624
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<pre style="margin: 0;">-<span id="LC1624" class="line" lang="mosel"></span>
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1625
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<pre style="margin: 0;">-<span id="LC1625" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1626
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1626" class="line" lang="mosel"> <span class="n" style="color: #333;">pamlTMP</span><span class="p">.</span><span class="n" style="color: #333;">Dec98</span><span class="p">.</span><span class="n" style="color: #333;">notes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1627
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<pre style="margin: 0;">-<span id="LC1627" class="line" lang="mosel"> <span class="p">===================</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1628
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<pre style="margin: 0;">-<span id="LC1628" class="line" lang="mosel"> <span class="n" style="color: #333;">Ziheng</span> <span class="n" style="color: #333;">Yang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1629
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<pre style="margin: 0;">-<span id="LC1629" class="line" lang="mosel"> <span class="n" style="color: #333;">Wed</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">9</span> <span class="m" style="color: #099;">10</span><span class="p">:</span><span class="m" style="color: #099;">44</span><span class="p">:</span><span class="m" style="color: #099;">37</span> <span class="n" style="color: #333;">GMT</span> <span class="m" style="color: #099;">1998</span></span>
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1630
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<pre style="margin: 0;">-<span id="LC1630" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1631
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<pre style="margin: 0;">-<span id="LC1631" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1632
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<pre style="margin: 0;">-<span id="LC1632" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">temporary</span> <span class="k" style="font-weight: 600;">version</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">paml</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">involved</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">changes</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1633
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<pre style="margin: 0;">-<span id="LC1633" class="line" lang="mosel"> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">quite</span> <span class="n" style="color: #333;">likely</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">errors</span><span class="p">.</span> <span class="n" style="color: #333;">Please</span> <span class="n" style="color: #333;">let</span> <span class="n" style="color: #333;">me</span> <span class="n" style="color: #333;">know</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">notice</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1634
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1634" class="line" lang="mosel"> <span class="n" style="color: #333;">anything</span> <span class="n" style="color: #333;">strange</span><span class="p">.</span> <span class="n" style="color: #333;">Some</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">options</span> <span class="k" style="font-weight: 600;">do</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">now</span><span class="p">.</span> <span class="n" style="color: #333;">Details</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1635
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<pre style="margin: 0;">-<span id="LC1635" class="line" lang="mosel"> <span class="n" style="color: #333;">follow</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">will</span> <span class="nf" style="color: #900; font-weight: 600;">compile</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Win32</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">PowerMac</span> <span class="n" style="color: #333;">versions</span> <span class="n" style="color: #333;">after</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1636
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1636" class="line" lang="mosel"> <span class="n" style="color: #333;">everything</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">tested</span><span class="p">.</span></span>
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1637
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<pre style="margin: 0;">-<span id="LC1637" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1638
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1638" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">Missing</span> <span class="n" style="color: #333;">data</span><span class="p">:</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">handle</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">data</span><span class="p">.</span> <span class="n" style="color: #333;">Choose</span></span>
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1639
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<pre style="margin: 0;">-<span id="LC1639" class="line" lang="mosel"> <span class="n" style="color: #333;">DelMissing</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">control</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ambiguity</span></span>
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1640
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<pre style="margin: 0;">-<span id="LC1640" class="line" lang="mosel"> <span class="n" style="color: #333;">characters</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">alignment</span> <span class="n" style="color: #333;">gaps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">did</span> <span class="n" style="color: #333;">previous</span> <span class="n" style="color: #333;">versions</span><span class="p">.</span></span>
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1641
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<pre style="margin: 0;">-<span id="LC1641" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1642
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1642" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">Clock</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">clock</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">crash</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span></span>
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1643
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1643" class="line" lang="mosel"> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">worse</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">no</span><span class="p">-</span><span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">definitions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">node</span></span>
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1644
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<pre style="margin: 0;">-<span id="LC1644" class="line" lang="mosel"> <span class="n" style="color: #333;">times</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">different</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">documentation</span></span>
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1645
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<pre style="margin: 0;">-<span id="LC1645" class="line" lang="mosel"> <span class="p">(</span><span class="n" style="color: #333;">pamlDOC</span><span class="p">.</span><span class="n" style="color: #333;">html</span><span class="p">),</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">tree</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1646
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<pre style="margin: 0;">-<span id="LC1646" class="line" lang="mosel"> <span class="n" style="color: #333;">topology</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Jeff</span> <span class="n" style="color: #333;">Thorne</span><span class="p">.</span></span>
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1647
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<pre style="margin: 0;">-<span id="LC1647" class="line" lang="mosel"></span>
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1648
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<pre style="margin: 0;">-<span id="LC1648" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">Nexus</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">formats</span><span class="p">:</span> <span class="n" style="color: #333;">Paml</span> <span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">now</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">tree</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1649
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<pre style="margin: 0;">-<span id="LC1649" class="line" lang="mosel"> <span class="n" style="color: #333;">structure</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Nexus</span> <span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">paup</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">MacClade</span><span class="p">.</span> <span class="n" style="color: #333;">Only</span></span>
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1650
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<pre style="margin: 0;">-<span id="LC1650" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">are</span> <span class="nb" style="color: #0086b3;">read</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">everything</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">ignored</span><span class="p">.</span></span>
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1651
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<pre style="margin: 0;">-<span id="LC1651" class="line" lang="mosel"></span>
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1652
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<pre style="margin: 0;">-<span id="LC1652" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">Ancestral</span> <span class="n" style="color: #333;">reconstruction</span><span class="p">:</span> <span class="n" style="color: #333;">Marginal</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">reconstructions</span> <span class="n" style="color: #333;">are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1653
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1653" class="line" lang="mosel"> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">done</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span><span class="p">-</span><span class="n" style="color: #333;">rates</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">constant</span><span class="p">-</span><span class="n" style="color: #333;">rate</span></span>
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1654
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1654" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span><span class="p">.</span> <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">protein</span><span class="p">-</span><span class="n" style="color: #333;">coding</span> <span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="n" style="color: #333;">reconstructions</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">done</span> <span class="n" style="color: #333;">at</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1655
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<pre style="margin: 0;">-<span id="LC1655" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nucleotide</span> <span class="n" style="color: #333;">level</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">baseml</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">particular</span><span class="p">,</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">that</span></span>
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1656
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<pre style="margin: 0;">-<span id="LC1656" class="line" lang="mosel"> <span class="n" style="color: #333;">account</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">differences</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">positions</span><span class="p">),</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">amino</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1657
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1657" class="line" lang="mosel"> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">level</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">aaml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">level</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">aaml</span><span class="p">.</span> <span class="n" style="color: #333;">According</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1658
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1658" class="line" lang="mosel"> <span class="n" style="color: #333;">Belinda</span> <span class="n" style="color: #333;">Chang</span><span class="p">,</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">reconstructions</span> <span class="n" style="color: #333;">tend</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">similar</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1659
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1659" class="line" lang="mosel"> <span class="n" style="color: #333;">Results</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">listed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">site</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">not</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1660
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1660" class="line" lang="mosel"> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">pattern</span> <span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">versions</span><span class="p">.</span> <span class="n" style="color: #333;">Missing</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">handled</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1661
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1661" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">analysis</span><span class="p">.</span> <span class="n" style="color: #333;">See</span> <span class="n" style="color: #333;">instructions</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">doc</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">baseml</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1662
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1662" class="line" lang="mosel"> <span class="n" style="color: #333;">more</span> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span> <span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Belinda</span> <span class="n" style="color: #333;">Chang</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">like</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">take</span> <span class="n" style="color: #333;">this</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1663
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1663" class="line" lang="mosel"> <span class="n" style="color: #333;">opportunity</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">point</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reconstructed</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">sequences</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1664
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1664" class="line" lang="mosel"> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">real</span> <span class="n" style="color: #333;">observed</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">errors</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1665
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1665" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1666
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1666" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">disabled</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1667
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1667" class="line" lang="mosel"> <span class="n" style="color: #333;">combination</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">lineages</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">codonml</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1668
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1668" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">never</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">implemented</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">not</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1669
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1669" class="line" lang="mosel"> <span class="n" style="color: #333;">disabled</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1670
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1670" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1671
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1671" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">Distance</span> <span class="n" style="color: #333;">matrices</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">codonml</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">codonml</span> <span class="n" style="color: #333;">outputs</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1672
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1672" class="line" lang="mosel"> <span class="n" style="color: #333;">matrices</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">synonymous</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nonsynonymous</span> <span class="n" style="color: #333;">rates</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">pairwise</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1673
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<pre style="margin: 0;">-<span id="LC1673" class="line" lang="mosel"> <span class="n" style="color: #333;">comparisons</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">method</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Nei</span> <span class="p">&</span> <span class="n" style="color: #333;">Gojobori</span> <span class="p">(</span><span class="m" style="color: #099;">1986</span><span class="p">)</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">files</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1674
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<pre style="margin: 0;">-<span id="LC1674" class="line" lang="mosel"> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">DistanceNG</span><span class="p">.</span><span class="n" style="color: #333;">dN</span> <span class="p">&</span> <span class="n" style="color: #333;">DistanceNG</span><span class="p">.</span><span class="n" style="color: #333;">dN</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">matrices</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">lower</span><span class="p">-</span><span class="n" style="color: #333;">diagonal</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1675
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1675" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">programs</span><span class="p">,</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">neighbor</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fitch</span><span class="p">,</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">phylip</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1676
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1676" class="line" lang="mosel"> <span class="p">(</span><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">possibly</span> <span class="n" style="color: #333;">paup</span><span class="p">*</span> <span class="n" style="color: #333;">too</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">reconstruction</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">length</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1677
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1677" class="line" lang="mosel"> <span class="n" style="color: #333;">estimation</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">methods</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">choose</span> <span class="n" style="color: #333;">runmode</span> <span class="p">=</span> <span class="p">-</span><span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">ML</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1678
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1678" class="line" lang="mosel"> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">comparison</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">matrices</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">ML</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1679
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1679" class="line" lang="mosel"> <span class="n" style="color: #333;">estimates</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">named</span> <span class="n" style="color: #333;">DistanceML</span><span class="p">.</span><span class="n" style="color: #333;">dS</span> <span class="p">&</span> <span class="n" style="color: #333;">DistanceML</span><span class="p">.</span><span class="n" style="color: #333;">dN</span><span class="p">,</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1680
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1680" class="line" lang="mosel"> <span class="n" style="color: #333;">synonymous</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nonsynonymous</span> <span class="n" style="color: #333;">rates</span><span class="p">.</span> <span class="n" style="color: #333;">Since</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">users</span> <span class="n" style="color: #333;">seem</span> <span class="n" style="color: #333;">interested</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1681
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1681" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">looking</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">lineages</span><span class="p">,</span> <span class="n" style="color: #333;">examination</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1682
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1682" class="line" lang="mosel"> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">shapes</span> <span class="n" style="color: #333;">indicated</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">branch</span> <span class="n" style="color: #333;">lengths</span> <span class="n" style="color: #333;">calculated</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">rates</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1683
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1683" class="line" lang="mosel"> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">interesting</span> <span class="n" style="color: #333;">although</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">intuitive</span><span class="p">.</span> <span class="n" style="color: #333;">Obviously</span><span class="p">,</span> <span class="n" style="color: #333;">you</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1684
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1684" class="line" lang="mosel"> <span class="n" style="color: #333;">should</span> <span class="k" style="font-weight: 600;">NOT</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">own</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">names</span><span class="p">;</span> <span class="n" style="color: #333;">otherwise</span> <span class="n" style="color: #333;">they</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1685
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1685" class="line" lang="mosel"> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">overwritten</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">species</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">10</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1686
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1686" class="line" lang="mosel"> <span class="n" style="color: #333;">characters</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">edit</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cut</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">names</span> <span class="n" style="color: #333;">short</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1687
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1687" class="line" lang="mosel"> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">Phylip</span> <span class="n" style="color: #333;">programs</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">decided</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">leave</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">work</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1688
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1688" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">plan</span> <span class="k" style="font-weight: 600;">to</span> <span class="nb" style="color: #0086b3;">create</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1689
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<pre style="margin: 0;">-<span id="LC1689" class="line" lang="mosel"> <span class="n" style="color: #333;">nucleotides</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acids</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span><span class="p">.</span></span>
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1690
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<pre style="margin: 0;">-<span id="LC1690" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1691
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<pre style="margin: 0;">-<span id="LC1691" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">An</span> <span class="n" style="color: #333;">minor</span> <span class="n" style="color: #333;">prompt</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">codonml</span> <span class="k" style="font-weight: 600;">with</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="p">(</span><span class="n" style="color: #333;">variable</span></span>
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1692
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<pre style="margin: 0;">-<span id="LC1692" class="line" lang="mosel"> <span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">lineages</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">set</span></span>
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1693
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<pre style="margin: 0;">-<span id="LC1693" class="line" lang="mosel"> <span class="n" style="color: #333;">lysozymeSmall</span><span class="p">.</span><span class="n" style="color: #333;">nuc</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">included</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">duplicate</span> <span class="n" style="color: #333;">my</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1694
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<pre style="margin: 0;">-<span id="LC1694" class="line" lang="mosel"> <span class="n" style="color: #333;">Yang</span> <span class="p">(</span><span class="m" style="color: #099;">1998</span> <span class="n" style="color: #333;">Molecular</span> <span class="n" style="color: #333;">Biology</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Evolution</span> <span class="m" style="color: #099;">15</span><span class="p">:</span> <span class="m" style="color: #099;">568</span><span class="p">-</span><span class="m" style="color: #099;">573</span><span class="p">).</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">control</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1695
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<pre style="margin: 0;">-<span id="LC1695" class="line" lang="mosel"> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">codemlLysozyme</span><span class="p">.</span><span class="n" style="color: #333;">ctl</span> <span class="n" style="color: #333;">explains</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">detail</span> <span class="n" style="color: #333;">how</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1696
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<pre style="margin: 0;">-<span id="LC1696" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">like</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">remind</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">correct</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1697
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<pre style="margin: 0;">-<span id="LC1697" class="line" lang="mosel"> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">estimate</span> <span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">branches</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">find</span> <span class="n" style="color: #333;">out</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1698
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<pre style="margin: 0;">-<span id="LC1698" class="line" lang="mosel"> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">one</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">then</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">test</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1699
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1699" class="line" lang="mosel"> <span class="n" style="color: #333;">whether</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">ratio</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">significantly</span> <span class="n" style="color: #333;">greater</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">one</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">problem</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1700
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<pre style="margin: 0;">-<span id="LC1700" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">such</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hypothesis</span> <span class="n" style="color: #333;">being</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">derived</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1701
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<pre style="margin: 0;">-<span id="LC1701" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hypothesis</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">result</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1702
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1702" class="line" lang="mosel"> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">tend</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">significantly</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">too</span> <span class="n" style="color: #333;">often</span><span class="p">.</span> <span class="n" style="color: #333;">Strictly</span> <span class="n" style="color: #333;">speaking</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1703
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<pre style="margin: 0;">-<span id="LC1703" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hypothesis</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">formulated</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">analysed</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1704
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1704" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1705
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<pre style="margin: 0;">-<span id="LC1705" class="line" lang="mosel"> <span class="n" style="color: #333;">Things</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">do</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">version</span> <span class="k" style="font-weight: 600;">include</span></span>
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1706
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<pre style="margin: 0;">-<span id="LC1706" class="line" lang="mosel"></span>
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1707
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<pre style="margin: 0;">-<span id="LC1707" class="line" lang="mosel"> <span class="p">.</span> <span class="n" style="color: #333;">All</span> <span class="n" style="color: #333;">parsimony</span><span class="p">-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">analyses</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">broken</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">pamp</span> <span class="n" style="color: #333;">is</span></span>
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1708
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<pre style="margin: 0;">-<span id="LC1708" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">included</span><span class="p">.</span> <span class="n" style="color: #333;">Programs</span> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">calculate</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">MP</span></span>
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1709
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<pre style="margin: 0;">-<span id="LC1709" class="line" lang="mosel"> <span class="n" style="color: #333;">score</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">tree</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">doing</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">ML</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span> <span class="n" style="color: #333;">Now</span> <span class="n" style="color: #333;">a</span></span>
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1710
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<pre style="margin: 0;">-<span id="LC1710" class="line" lang="mosel"> <span class="p">-</span><span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">indicate</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">possible</span><span class="p">.</span></span>
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1711
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<pre style="margin: 0;">-<span id="LC1711" class="line" lang="mosel"></span>
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1712
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<pre style="margin: 0;">-<span id="LC1712" class="line" lang="mosel"></span>
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1713
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<pre style="margin: 0;">-<span id="LC1713" class="line" lang="mosel"></span>
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1714
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<pre style="margin: 0;">-<span id="LC1714" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">1.4</span> <span class="p">(</span><span class="n" style="color: #333;">UCL</span><span class="p">)</span></span>
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1715
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<pre style="margin: 0;">-<span id="LC1715" class="line" lang="mosel"><span class="n" style="color: #333;">July</span> <span class="m" style="color: #099;">1998</span> </span>
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1716
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<pre style="margin: 0;">-<span id="LC1716" class="line" lang="mosel"></span>
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1717
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<pre style="margin: 0;">-<span id="LC1717" class="line" lang="mosel"> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">Most</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">are</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">codeml</span> <span class="p">(</span><span class="n" style="color: #333;">aaml</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">amino</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1718
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<pre style="margin: 0;">-<span id="LC1718" class="line" lang="mosel"> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codonml</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">sequences</span><span class="p">).</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1719
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<pre style="margin: 0;">-<span id="LC1719" class="line" lang="mosel"> <span class="n" style="color: #333;">codon</span> <span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">implemented</span> <span class="p">(</span><span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Nielsen</span> <span class="m" style="color: #099;">1998</span><span class="p">;</span> <span class="n" style="color: #333;">Nielsen</span></span>
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1720
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<pre style="margin: 0;">-<span id="LC1720" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span> <span class="m" style="color: #099;">1998</span><span class="p">;</span> <span class="n" style="color: #333;">Yang</span> <span class="m" style="color: #099;">1998</span><span class="p">).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1721
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<pre style="margin: 0;">-<span id="LC1721" class="line" lang="mosel"> <span class="m" style="color: #099;">2.</span> <span class="n" style="color: #333;">Some</span> <span class="n" style="color: #333;">problems</span> <span class="n" style="color: #333;">relating</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">reconstruction</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span></span>
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1722
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1722" class="line" lang="mosel"> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">fixed</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">earlier</span> <span class="n" style="color: #333;">algorithm</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1723
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1723" class="line" lang="mosel"> <span class="n" style="color: #333;">properly</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">sequences</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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1724
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<pre style="margin: 0;">-<span id="LC1724" class="line" lang="mosel"> <span class="n" style="color: #333;">algorithm</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">guess</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">likely</span> <span class="n" style="color: #333;">character</span> <span class="n" style="color: #333;">states</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">interior</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1725
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<pre style="margin: 0;">-<span id="LC1725" class="line" lang="mosel"> <span class="n" style="color: #333;">nodes</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">then</span> <span class="k" style="font-weight: 600;">uses</span> <span class="n" style="color: #333;">those</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">generate</span> <span class="n" style="color: #333;">reconstructions</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1726
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1726" class="line" lang="mosel"> <span class="p">(</span><span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">reconstructions</span><span class="p">,</span> <span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">eq</span><span class="p">.</span> <span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Yang</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="m" style="color: #099;">1995</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1727
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1727" class="line" lang="mosel"> <span class="n" style="color: #333;">evaluated</span><span class="p">.</span> <span class="n" style="color: #333;">Sometimes</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">strategy</span> <span class="n" style="color: #333;">misses</span> <span class="n" style="color: #333;">important</span> <span class="n" style="color: #333;">reconstructions</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1728
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1728" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">probabilities</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">reconstructed</span> <span class="n" style="color: #333;">characters</span> <span class="n" style="color: #333;">at</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1729
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1729" class="line" lang="mosel"> <span class="n" style="color: #333;">specific</span> <span class="n" style="color: #333;">interior</span> <span class="n" style="color: #333;">nodes</span> <span class="p">(</span><span class="n" style="color: #333;">marginal</span> <span class="n" style="color: #333;">reconstructions</span><span class="p">;</span> <span class="n" style="color: #333;">see</span> <span class="n" style="color: #333;">eq</span><span class="p">.</span> <span class="m" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Yang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1730
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1730" class="line" lang="mosel"> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="m" style="color: #099;">1995</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">substantially</span> <span class="n" style="color: #333;">underestimated</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1731
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1731" class="line" lang="mosel"> <span class="n" style="color: #333;">sequences</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">small</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">written</span> <span class="n" style="color: #333;">separate</span> <span class="n" style="color: #333;">codes</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1732
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1732" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">marginal</span> <span class="n" style="color: #333;">reconstruction</span><span class="p">,</span> <span class="n" style="color: #333;">evaluating</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">possible</span> <span class="n" style="color: #333;">character</span> <span class="n" style="color: #333;">states</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1733
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1733" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">interior</span> <span class="n" style="color: #333;">node</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">works</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1734
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1734" class="line" lang="mosel"> <span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">sites</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">feature</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">was</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">implemented</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1735
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1735" class="line" lang="mosel"> <span class="n" style="color: #333;">before</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">joint</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">works</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">sites</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1736
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1736" class="line" lang="mosel"> <span class="n" style="color: #333;">only</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">old</span> <span class="n" style="color: #333;">problem</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">possibly</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">important</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1737
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1737" class="line" lang="mosel"> <span class="n" style="color: #333;">reconstructions</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">posterior</span> <span class="n" style="color: #333;">probabilities</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">those</span> <span class="n" style="color: #333;">joint</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1738
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1738" class="line" lang="mosel"> <span class="n" style="color: #333;">reconstructions</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">evaluated</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">accurate</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">an</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1739
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1739" class="line" lang="mosel"> <span class="n" style="color: #333;">option</span> <span class="p">(</span><span class="n" style="color: #333;">choose</span> <span class="n" style="color: #333;">RateAncestor</span> <span class="p">=</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">user</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">specify</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1740
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1740" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reconstruction</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">evaluated</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">approaches</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">expected</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1741
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<pre style="margin: 0;">-<span id="LC1741" class="line" lang="mosel"> <span class="n" style="color: #333;">produce</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">similar</span> <span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">since</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">marginal</span> <span class="n" style="color: #333;">reconstruction</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1742
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1742" class="line" lang="mosel"> <span class="n" style="color: #333;">always</span> <span class="n" style="color: #333;">reliable</span><span class="p">,</span> <span class="n" style="color: #333;">perhaps</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">always</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">analysis</span><span class="p">.</span></span>
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1743
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<pre style="margin: 0;">-<span id="LC1743" class="line" lang="mosel"> <span class="p">(</span><span class="n" style="color: #333;">Thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Belinda</span> <span class="n" style="color: #333;">Chang</span><span class="p">.)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1744
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<pre style="margin: 0;">-<span id="LC1744" class="line" lang="mosel"> <span class="m" style="color: #099;">3.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">estimated</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">sites</span> <span class="n" style="color: #333;">under</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1745
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<pre style="margin: 0;">-<span id="LC1745" class="line" lang="mosel"> <span class="n" style="color: #333;">variable</span><span class="p">-</span><span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="s2" style="color: #d14;">"Rates.out"</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="s2" style="color: #d14;">"rst"</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1746
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1746" class="line" lang="mosel"> <span class="m" style="color: #099;">4.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">ancestral</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">reconstructions</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1747
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1747" class="line" lang="mosel"> <span class="n" style="color: #333;">codon</span><span class="p">-</span><span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">codonml</span><span class="p">).</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">has</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">tested</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1748
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1748" class="line" lang="mosel"> <span class="n" style="color: #333;">carefully</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">appreciate</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">comments</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">it</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1749
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<pre style="margin: 0;">-<span id="LC1749" class="line" lang="mosel"> <span class="m" style="color: #099;">5.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">minor</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">made</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">several</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1750
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1750" class="line" lang="mosel"> <span class="n" style="color: #333;">floating</span> <span class="n" style="color: #333;">exception</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">seem</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">occur</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">DEC</span> <span class="n" style="color: #333;">Alpha</span> <span class="n" style="color: #333;">machines</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1751
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1751" class="line" lang="mosel"> <span class="n" style="color: #333;">only</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1752
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1752" class="line" lang="mosel"> <span class="m" style="color: #099;">6.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">documentation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">changed</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">html</span> <span class="n" style="color: #333;">format</span><span class="p">.</span> </span>
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1753
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1753" class="line" lang="mosel"></span>
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1754
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<pre style="margin: 0;">-<span id="LC1754" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1755
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<pre style="margin: 0;">-<span id="LC1755" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1756
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<pre style="margin: 0;">-<span id="LC1756" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">1.3</span><span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">c</span> <span class="p">(</span><span class="n" style="color: #333;">UCL</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1757
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1757" class="line" lang="mosel"><span class="n" style="color: #333;">June</span> <span class="m" style="color: #099;">1998</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1758
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<pre style="margin: 0;">-<span id="LC1758" class="line" lang="mosel"></span>
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1759
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<pre style="margin: 0;">-<span id="LC1759" class="line" lang="mosel"> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">Basemlg</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">put</span> <span class="n" style="color: #333;">back</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">request</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">user</span><span class="p">.</span></span>
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1760
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<pre style="margin: 0;">-<span id="LC1760" class="line" lang="mosel"></span>
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1761
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<pre style="margin: 0;">-<span id="LC1761" class="line" lang="mosel"> <span class="m" style="color: #099;">2.</span> <span class="n" style="color: #333;">Some</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">made</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">codeml</span> <span class="n" style="color: #333;">concerning</span> <span class="n" style="color: #333;">codon</span><span class="p">-</span><span class="n" style="color: #333;">substitution</span></span>
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1762
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<pre style="margin: 0;">-<span id="LC1762" class="line" lang="mosel"> <span class="n" style="color: #333;">models</span> <span class="p">(</span><span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Nielsen</span> <span class="m" style="color: #099;">1998</span> <span class="n" style="color: #333;">JME</span><span class="p">;</span> <span class="n" style="color: #333;">Yang</span> <span class="m" style="color: #099;">1998</span> <span class="n" style="color: #333;">MBE</span><span class="p">;</span> <span class="n" style="color: #333;">Nielsen</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span></span>
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1763
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<pre style="margin: 0;">-<span id="LC1763" class="line" lang="mosel"> <span class="m" style="color: #099;">1998</span> <span class="n" style="color: #333;">Genetics</span><span class="p">)</span></span>
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1764
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<pre style="margin: 0;">-<span id="LC1764" class="line" lang="mosel"></span>
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1765
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<pre style="margin: 0;">-<span id="LC1765" class="line" lang="mosel"></span>
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1766
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<pre style="margin: 0;">-<span id="LC1766" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1767
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<pre style="margin: 0;">-<span id="LC1767" class="line" lang="mosel"><span class="n" style="color: #333;">PAML</span> <span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">1.3</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">UC</span> <span class="n" style="color: #333;">Berkeley</span><span class="p">)</span></span>
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1768
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<pre style="margin: 0;">-<span id="LC1768" class="line" lang="mosel"><span class="n" style="color: #333;">July</span> <span class="m" style="color: #099;">1997</span> </span>
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1769
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<pre style="margin: 0;">-<span id="LC1769" class="line" lang="mosel"></span>
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1770
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<pre style="margin: 0;">-<span id="LC1770" class="line" lang="mosel"> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">Starting</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">version</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">basemlg</span> <span class="n" style="color: #333;">will</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1771
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<pre style="margin: 0;">-<span id="LC1771" class="line" lang="mosel"> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">package</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">implements</span> <span class="n" style="color: #333;">the</span> <span class="p">(</span><span class="n" style="color: #333;">continuous</span><span class="p">)</span></span>
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1772
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1772" class="line" lang="mosel"> <span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">variation</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">nucleotide</span> <span class="n" style="color: #333;">sites</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1773
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<pre style="margin: 0;">-<span id="LC1773" class="line" lang="mosel"> <span class="p">(</span><span class="n" style="color: #333;">Yang</span> <span class="m" style="color: #099;">1993</span><span class="p">).</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">involves</span> <span class="n" style="color: #333;">intensive</span> <span class="n" style="color: #333;">computation</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1774
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<pre style="margin: 0;">-<span id="LC1774" class="line" lang="mosel"> <span class="n" style="color: #333;">superseded</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">discrete</span><span class="p">-</span><span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">implemented</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1775
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<pre style="margin: 0;">-<span id="LC1775" class="line" lang="mosel"> <span class="n" style="color: #333;">baseml</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">want</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">program</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">previous</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1776
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<pre style="margin: 0;">-<span id="LC1776" class="line" lang="mosel"> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">paml</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">obtained</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">me</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nowhere</span> <span class="k" style="font-weight: 600;">else</span><span class="p">.</span></span>
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1777
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<pre style="margin: 0;">-<span id="LC1777" class="line" lang="mosel"></span>
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1778
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<pre style="margin: 0;">-<span id="LC1778" class="line" lang="mosel"> <span class="m" style="color: #099;">2.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">simulation</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">mcml</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">removed</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">package</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1779
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<pre style="margin: 0;">-<span id="LC1779" class="line" lang="mosel"> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">superced</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">listtree</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">does</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">things</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1780
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<pre style="margin: 0;">-<span id="LC1780" class="line" lang="mosel"> <span class="n" style="color: #333;">besides</span> <span class="n" style="color: #333;">simulating</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">sets</span><span class="p">.</span></span>
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1781
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<pre style="margin: 0;">-<span id="LC1781" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1782
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1782" class="line" lang="mosel"> <span class="m" style="color: #099;">3.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">stepwise</span> <span class="n" style="color: #333;">addition</span> <span class="n" style="color: #333;">algorithm</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">programs</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1783
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1783" class="line" lang="mosel"> <span class="n" style="color: #333;">baseml</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">codeml</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">algorithm</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">faster</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1784
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1784" class="line" lang="mosel"> <span class="n" style="color: #333;">star</span><span class="p">-</span><span class="n" style="color: #333;">decomposition</span> <span class="n" style="color: #333;">algorithm</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">before</span><span class="p">,</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">my</span> <span class="n" style="color: #333;">implementation</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1785
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1785" class="line" lang="mosel"> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">crude</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">inefficient</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">NNI</span> <span class="n" style="color: #333;">perturbation</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">implemented</span> <span class="n" style="color: #333;">too</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1786
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<pre style="margin: 0;">-<span id="LC1786" class="line" lang="mosel"> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">molecular</span> <span class="n" style="color: #333;">clock</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1787
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<pre style="margin: 0;">-<span id="LC1787" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1788
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<pre style="margin: 0;">-<span id="LC1788" class="line" lang="mosel"> <span class="m" style="color: #099;">4.</span> <span class="n" style="color: #333;">Many</span> <span class="n" style="color: #333;">changes</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">made</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">codonml</span> <span class="p">(</span><span class="n" style="color: #333;">codeml</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1789
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1789" class="line" lang="mosel"> <span class="n" style="color: #333;">seqtype</span><span class="p">=</span><span class="m" style="color: #099;">1</span><span class="p">).</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">few</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">codon</span><span class="p">-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">implemented</span><span class="p">.</span> <span class="n" style="color: #333;">One</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1790
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1790" class="line" lang="mosel"> <span class="n" style="color: #333;">assumes</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">nonsynonymous</span><span class="p">/</span><span class="n" style="color: #333;">synonymous</span> <span class="p">(</span><span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span><span class="p">)</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">ratios</span> <span class="n" style="color: #333;">among</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1791
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1791" class="line" lang="mosel"> <span class="n" style="color: #333;">branches</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">phylogeny</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">useful</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">detecting</span> <span class="n" style="color: #333;">episodic</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1792
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1792" class="line" lang="mosel"> <span class="n" style="color: #333;">positive</span> <span class="n" style="color: #333;">selection</span><span class="p">.</span> <span class="n" style="color: #333;">Another</span> <span class="n" style="color: #333;">allows</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">dN</span><span class="p">/</span><span class="n" style="color: #333;">dS</span> <span class="n" style="color: #333;">ratio</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">vary</span> <span class="n" style="color: #333;">among</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1793
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1793" class="line" lang="mosel"> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">useful</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">neutrality</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">detecting</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1794
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1794" class="line" lang="mosel"> <span class="n" style="color: #333;">positively</span><span class="p">-</span><span class="n" style="color: #333;">selected</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span><span class="p">.</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">my</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1795
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<pre style="margin: 0;">-<span id="LC1795" class="line" lang="mosel"> <span class="n" style="color: #333;">collaborative</span> <span class="n" style="color: #333;">work</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Rasmus</span> <span class="n" style="color: #333;">Nielsen</span><span class="p">.</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">made</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">changes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span></span>
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1796
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<pre style="margin: 0;">-<span id="LC1796" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">estimates</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">dS</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">dN</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairwise</span> <span class="n" style="color: #333;">comparisons</span> <span class="p">(</span><span class="n" style="color: #333;">codonml</span> <span class="k" style="font-weight: 600;">with</span></span>
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1797
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<pre style="margin: 0;">-<span id="LC1797" class="line" lang="mosel"> <span class="n" style="color: #333;">runmode</span><span class="p">=-</span><span class="m" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">results</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">easy</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">understand</span><span class="p">.</span> <span class="n" style="color: #333;">Another</span></span>
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1798
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<pre style="margin: 0;">-<span id="LC1798" class="line" lang="mosel"> <span class="n" style="color: #333;">change</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">program</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">codon</span><span class="p">-</span><span class="n" style="color: #333;">substitution</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Goldman</span></span>
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1799
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<pre style="margin: 0;">-<span id="LC1799" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span> <span class="p">(</span><span class="m" style="color: #099;">1994</span><span class="p">).</span> <span class="n" style="color: #333;">We</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Grantham</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1800
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<pre style="margin: 0;">-<span id="LC1800" class="line" lang="mosel"> <span class="p">(</span><span class="m" style="color: #099;">1974</span><span class="p">)</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">modify</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rate</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">nonsynonymous</span> <span class="n" style="color: #333;">substitutions</span><span class="p">,</span> <span class="n" style="color: #333;">but</span></span>
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1801
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<pre style="margin: 0;">-<span id="LC1801" class="line" lang="mosel"> <span class="n" style="color: #333;">unfortunately</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">fit</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">well</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">always</span></span>
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1802
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<pre style="margin: 0;">-<span id="LC1802" class="line" lang="mosel"> <span class="n" style="color: #333;">fit</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">better</span> <span class="n" style="color: #333;">than</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">simply</span> <span class="n" style="color: #333;">assume</span> <span class="n" style="color: #333;">equal</span> <span class="n" style="color: #333;">distance</span> <span class="n" style="color: #333;">between</span></span>
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1803
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<pre style="margin: 0;">-<span id="LC1803" class="line" lang="mosel"> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">two</span> <span class="n" style="color: #333;">amino</span> <span class="n" style="color: #333;">acids</span><span class="p">.</span> <span class="n" style="color: #333;">So</span> <span class="n" style="color: #333;">I</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">option</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">ignoring</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">amino</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1804
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<pre style="margin: 0;">-<span id="LC1804" class="line" lang="mosel"> <span class="n" style="color: #333;">acid</span> <span class="n" style="color: #333;">differences</span><span class="p">.</span> <span class="n" style="color: #333;">Goldman</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Yang</span><span class="s1" style="color: #d14;">'s original formula is still</span></span>
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1805
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<pre style="margin: 0;">-<span id="LC1805" class="line" lang="mosel"><span class="s1" style="color: #d14;"> available but not recommended for use. As a result of these changes,</span></span>
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1806
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<pre style="margin: 0;">-<span id="LC1806" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the formulation of the Goldman and Yang model is now somewhat</span></span>
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1807
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<pre style="margin: 0;">-<span id="LC1807" class="line" lang="mosel"><span class="s1" style="color: #d14;"> different from the paper and previous versions of the program. See</span></span>
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1808
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<pre style="margin: 0;">-<span id="LC1808" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Section 6.2 for details.</span></span>
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1809
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<pre style="margin: 0;">-<span id="LC1809" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1810
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<pre style="margin: 0;">-<span id="LC1810" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 5. I have again made some changes with the user interface, based on my</span></span>
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1811
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<pre style="margin: 0;">-<span id="LC1811" class="line" lang="mosel"><span class="s1" style="color: #d14;"> guess of what the "user" would like to see.</span></span>
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1812
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<pre style="margin: 0;">-<span id="LC1812" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1813
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<pre style="margin: 0;">-<span id="LC1813" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1814
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<pre style="margin: 0;">-<span id="LC1814" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1815
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<pre style="margin: 0;">-<span id="LC1815" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 1.1a-d: (University of California, Berkeley)</span></span>
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1816
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<pre style="margin: 0;">-<span id="LC1816" class="line" lang="mosel"><span class="s1" style="color: #d14;">1995-1996 </span></span>
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1817
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<pre style="margin: 0;">-<span id="LC1817" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1818
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<pre style="margin: 0;">-<span id="LC1818" class="line" lang="mosel"><span class="s1" style="color: #d14;">1.1a No records of changes remain.</span></span>
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1819
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<pre style="margin: 0;">-<span id="LC1819" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<pre style="margin: 0;">-<span id="LC1820" class="line" lang="mosel"><span class="s1" style="color: #d14;">1.1b November, 1995:</span></span>
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1821
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<pre style="margin: 0;">-<span id="LC1821" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1822
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<pre style="margin: 0;">-<span id="LC1822" class="line" lang="mosel"><span class="s1" style="color: #d14;">The following line at the beginning of the file tools.h </span></span>
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1823
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<pre style="margin: 0;">-<span id="LC1823" class="line" lang="mosel"><span class="s1" style="color: #d14;"> #define __cplusplus</span></span>
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1824
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<pre style="margin: 0;">-<span id="LC1824" class="line" lang="mosel"><span class="s1" style="color: #d14;">is removed. I added this line to avoid some (unjustified) warning</span></span>
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1825
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<pre style="margin: 0;">-<span id="LC1825" class="line" lang="mosel"><span class="s1" style="color: #d14;">messages from a compiler I used to use and forgot to remove it when I</span></span>
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1826
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<pre style="margin: 0;">-<span id="LC1826" class="line" lang="mosel"><span class="s1" style="color: #d14;">was preparing paml1.1. This line made some compilers unable to</span></span>
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<pre style="margin: 0;">-<span id="LC1827" class="line" lang="mosel"><span class="s1" style="color: #d14;">compile.</span></span>
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<pre style="margin: 0;">-<span id="LC1828" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1829
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<pre style="margin: 0;">-<span id="LC1829" class="line" lang="mosel"><span class="s1" style="color: #d14;">A bug that caused baseml and basemlg to give wrong estimates of kappa</span></span>
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1830
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<pre style="margin: 0;">-<span id="LC1830" class="line" lang="mosel"><span class="s1" style="color: #d14;">under the F84 model is now fixed. Estimates of kappa under the F84</span></span>
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1831
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<pre style="margin: 0;">-<span id="LC1831" class="line" lang="mosel"><span class="s1" style="color: #d14;">models listed in the paml 1.0 and 1.1 documents are all incorrect and</span></span>
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1832
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<pre style="margin: 0;">-<span id="LC1832" class="line" lang="mosel"><span class="s1" style="color: #d14;">are a bit too small. For example, the estimate of kappa under the F84</span></span>
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1833
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<pre style="margin: 0;">-<span id="LC1833" class="line" lang="mosel"><span class="s1" style="color: #d14;">model for the mtDNA data of Brown et al. (1982) should be 4.344 while</span></span>
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1834
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<pre style="margin: 0;">-<span id="LC1834" class="line" lang="mosel"><span class="s1" style="color: #d14;">the wrong estimate given in the large table of the document is 3.420.</span></span>
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1835
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<pre style="margin: 0;">-<span id="LC1835" class="line" lang="mosel"><span class="s1" style="color: #d14;">Likelihood value, branch lengths and other parameters seem to have</span></span>
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1836
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<pre style="margin: 0;">-<span id="LC1836" class="line" lang="mosel"><span class="s1" style="color: #d14;">been correctly calculated by paml 1.0 and 1.1. Versions prior to 1.0</span></span>
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1837
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<pre style="margin: 0;">-<span id="LC1837" class="line" lang="mosel"><span class="s1" style="color: #d14;">do not have this bug, and results in Yang (J. Mol. Evol. 1994,</span></span>
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1838
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<pre style="margin: 0;">-<span id="LC1838" class="line" lang="mosel"><span class="s1" style="color: #d14;">39:306-314) and Yang, Lauder, and Lin (J. Mol. Evol. 1995,</span></span>
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1839
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<pre style="margin: 0;">-<span id="LC1839" class="line" lang="mosel"><span class="s1" style="color: #d14;">41:587-596), where the F84 model was used, are correct.</span></span>
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1840
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<pre style="margin: 0;">-<span id="LC1840" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1841
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<pre style="margin: 0;">-<span id="LC1841" class="line" lang="mosel"><span class="s1" style="color: #d14;">1.1c March 1996 </span></span>
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1842
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<pre style="margin: 0;">-<span id="LC1842" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1843
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<pre style="margin: 0;">-<span id="LC1843" class="line" lang="mosel"><span class="s1" style="color: #d14;">Representation of tree topologies using branches (see the document)</span></span>
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1844
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<pre style="margin: 0;">-<span id="LC1844" class="line" lang="mosel"><span class="s1" style="color: #d14;">are now allowed (restored) in the tree structure file. This is for</span></span>
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1845
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<pre style="margin: 0;">-<span id="LC1845" class="line" lang="mosel"><span class="s1" style="color: #d14;">coping with cases where some taxa are ancestors of others. If this</span></span>
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1846
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<pre style="margin: 0;">-<span id="LC1846" class="line" lang="mosel"><span class="s1" style="color: #d14;">representation is used, the line starts with a dollar sign. So the</span></span>
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1847
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<pre style="margin: 0;">-<span id="LC1847" class="line" lang="mosel"><span class="s1" style="color: #d14;">following line in the file trees.5s (the tree file for 5 species)</span></span>
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1848
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<pre style="margin: 0;">-<span id="LC1848" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1849
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<pre style="margin: 0;">-<span id="LC1849" class="line" lang="mosel"><span class="s1" style="color: #d14;">$ 5 6 3 6 4 6 5 3 1 3 2</span></span>
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1850
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<pre style="margin: 0;">-<span id="LC1850" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1851
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<pre style="margin: 0;">-<span id="LC1851" class="line" lang="mosel"><span class="s1" style="color: #d14;">represents the tree ((12)34), with 5 to be the ancestor of 1 and 2.</span></span>
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1852
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<pre style="margin: 0;">-<span id="LC1852" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1853
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<pre style="margin: 0;">-<span id="LC1853" class="line" lang="mosel"><span class="s1" style="color: #d14;">Alignment gaps are now allowed when option G is used (for multiple</span></span>
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1854
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<pre style="margin: 0;">-<span id="LC1854" class="line" lang="mosel"><span class="s1" style="color: #d14;">genes). The gaps are removed before analysis.</span></span>
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1855
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<pre style="margin: 0;">-<span id="LC1855" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1856
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<pre style="margin: 0;">-<span id="LC1856" class="line" lang="mosel"><span class="s1" style="color: #d14;">A small program listtree lists all the bifurcating trees for a given</span></span>
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1857
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<pre style="margin: 0;">-<span id="LC1857" class="line" lang="mosel"><span class="s1" style="color: #d14;">(small) number of species.</span></span>
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1858
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<pre style="margin: 0;">-<span id="LC1858" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1859
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<pre style="margin: 0;">-<span id="LC1859" class="line" lang="mosel"><span class="s1" style="color: #d14;">codonml (codeml.c with seqtype=1) now has an option for calculating</span></span>
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1860
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<pre style="margin: 0;">-<span id="LC1860" class="line" lang="mosel"><span class="s1" style="color: #d14;">the number of synonymous substitutions per synonymous site (Ks) and</span></span>
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1861
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<pre style="margin: 0;">-<span id="LC1861" class="line" lang="mosel"><span class="s1" style="color: #d14;">the number of nonsynonymous substitutions per nonsynonymous site (Ka)</span></span>
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1862
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<pre style="margin: 0;">-<span id="LC1862" class="line" lang="mosel"><span class="s1" style="color: #d14;">and their ratio for each pairwise comparison, using the method of</span></span>
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1863
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<pre style="margin: 0;">-<span id="LC1863" class="line" lang="mosel"><span class="s1" style="color: #d14;">Goldman and Yang (1994). This is implemented with</span></span>
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1864
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<pre style="margin: 0;">-<span id="LC1864" class="line" lang="mosel"><span class="s1" style="color: #d14;">runmode=-2. Estimates of Ks and Ka are collected in the file rst and</span></span>
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1865
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<pre style="margin: 0;">-<span id="LC1865" class="line" lang="mosel"><span class="s1" style="color: #d14;">estimates of model parameters in the file mlc. This option produces</span></span>
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1866
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<pre style="margin: 0;">-<span id="LC1866" class="line" lang="mosel"><span class="s1" style="color: #d14;">table 2 in the Goldman & Yang paper.</span></span>
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1867
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<pre style="margin: 0;">-<span id="LC1867" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1868
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<pre style="margin: 0;">-<span id="LC1868" class="line" lang="mosel"><span class="s1" style="color: #d14;">The interior nodes were incorrectly identified when the ancestral</span></span>
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1869
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<pre style="margin: 0;">-<span id="LC1869" class="line" lang="mosel"><span class="s1" style="color: #d14;">sequences were listed in the file rst. They were all one less than</span></span>
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1870
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<pre style="margin: 0;">-<span id="LC1870" class="line" lang="mosel"><span class="s1" style="color: #d14;">their correct numbers. Nodes 7, 8, 9, 10 for the stewart.aa data were</span></span>
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1871
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<pre style="margin: 0;">-<span id="LC1871" class="line" lang="mosel"><span class="s1" style="color: #d14;">incorrectly identified as nodes 6, 7, 8, 9. This is corrected now.</span></span>
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1872
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<pre style="margin: 0;">-<span id="LC1872" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1873
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<pre style="margin: 0;">-<span id="LC1873" class="line" lang="mosel"><span class="s1" style="color: #d14;">1.1d. July 1996</span></span>
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1874
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<pre style="margin: 0;">-<span id="LC1874" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1875
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<pre style="margin: 0;">-<span id="LC1875" class="line" lang="mosel"><span class="s1" style="color: #d14;">An unintended version of codeml.c was included in version 1.1c, which</span></span>
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1876
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<pre style="margin: 0;">-<span id="LC1876" class="line" lang="mosel"><span class="s1" style="color: #d14;">causes the program to produce different results under the codon-based</span></span>
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1877
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<pre style="margin: 0;">-<span id="LC1877" class="line" lang="mosel"><span class="s1" style="color: #d14;">model of Goldman and Yang (1994). The small number in baseml.c was</span></span>
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1878
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<pre style="margin: 0;">-<span id="LC1878" class="line" lang="mosel"><span class="s1" style="color: #d14;">set too small, making the program do unnecessary iterations; this is</span></span>
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1879
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<pre style="margin: 0;">-<span id="LC1879" class="line" lang="mosel"><span class="s1" style="color: #d14;">fixed now. I also changed the program pamp so that it will estimate</span></span>
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1880
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<pre style="margin: 0;">-<span id="LC1880" class="line" lang="mosel"><span class="s1" style="color: #d14;">the substitution rate matrix without using a tree.</span></span>
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1881
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<pre style="margin: 0;">-<span id="LC1881" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1882
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<pre style="margin: 0;">-<span id="LC1882" class="line" lang="mosel"><span class="s1" style="color: #d14;">I have included a few other genetic code tables in this version of</span></span>
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1883
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<pre style="margin: 0;">-<span id="LC1883" class="line" lang="mosel"><span class="s1" style="color: #d14;">codeml; see the file codeml.ctl.</span></span>
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1884
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<pre style="margin: 0;">-<span id="LC1884" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1885
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<pre style="margin: 0;">-<span id="LC1885" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1886
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<pre style="margin: 0;">-<span id="LC1886" class="line" lang="mosel"><span class="s1" style="color: #d14;">PAML Version 1.2: November 1996 (UC Berkeley)</span></span>
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1887
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<pre style="margin: 0;">-<span id="LC1887" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1888
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<pre style="margin: 0;">-<span id="LC1888" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 1. I have done some changes with the user interface. Name of files</span></span>
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1889
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<pre style="margin: 0;">-<span id="LC1889" class="line" lang="mosel"><span class="s1" style="color: #d14;">(sequence data file, control file, tree structure file) are now</span></span>
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1890
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<pre style="margin: 0;">-<span id="LC1890" class="line" lang="mosel"><span class="s1" style="color: #d14;">specified in the control files (The default are baseml.ctl,</span></span>
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1891
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<pre style="margin: 0;">-<span id="LC1891" class="line" lang="mosel"><span class="s1" style="color: #d14;">codeml.ctl, pamp.ctl, mcmctree.ctl). The command line for executing a</span></span>
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1892
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<pre style="margin: 0;">-<span id="LC1892" class="line" lang="mosel"><span class="s1" style="color: #d14;">program is now ProgramName ControlFileName with ControlFileName</span></span>
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1893
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<pre style="margin: 0;">-<span id="LC1893" class="line" lang="mosel"><span class="s1" style="color: #d14;">optional. I have added some text in the output file of baseml so that</span></span>
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1894
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<pre style="margin: 0;">-<span id="LC1894" class="line" lang="mosel"><span class="s1" style="color: #d14;">the results are eassier to understand. Choose verbose=0 in the</span></span>
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1895
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<pre style="margin: 0;">-<span id="LC1895" class="line" lang="mosel"><span class="s1" style="color: #d14;">control file if you do not want the detailed output.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1896
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<pre style="margin: 0;">-<span id="LC1896" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1897
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1897" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 2. A new program mcmctree is included, which performs Bayesian</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1898
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<pre style="margin: 0;">-<span id="LC1898" class="line" lang="mosel"><span class="s1" style="color: #d14;">estimation of phylogenies using Markov chain Monte Carlo methods</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1899
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<pre style="margin: 0;">-<span id="LC1899" class="line" lang="mosel"><span class="s1" style="color: #d14;">(Rannala and Yang 1996; Yang and Rannala 1997).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1900
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<pre style="margin: 0;">-<span id="LC1900" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1901
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<pre style="margin: 0;">-<span id="LC1901" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 3. A number of minor changes are made, such as using species names</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1902
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<pre style="margin: 0;">-<span id="LC1902" class="line" lang="mosel"><span class="s1" style="color: #d14;">in the parenthesis tree representation.</span></span>
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1903
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<pre style="margin: 0;">-<span id="LC1903" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1904
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<pre style="margin: 0;">-<span id="LC1904" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1905
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<pre style="margin: 0;">-<span id="LC1905" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1906
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<pre style="margin: 0;">-<span id="LC1906" class="line" lang="mosel"><span class="s1" style="color: #d14;">July 1995 </span></span>
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1907
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1907" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 1.1: (IMEG PennState)</span></span>
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1908
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<pre style="margin: 0;">-<span id="LC1908" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1909
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1909" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Models for analyzing data of multiple genes (Yang 1996 JME) are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1910
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1910" class="line" lang="mosel"><span class="s1" style="color: #d14;"> implemented in baseml and codeml. Two more programs are included:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1911
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<pre style="margin: 0;">-<span id="LC1911" class="line" lang="mosel"><span class="s1" style="color: #d14;"> pamp for parsimony-based analysis implementing the methods of Yang and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1912
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<pre style="margin: 0;">-<span id="LC1912" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Kumar (1996 MBE) and mcml for Monte Carlo simulation (prepared for</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1913
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<pre style="margin: 0;">-<span id="LC1913" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Arndt von Haeseler but apparently not used).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1914
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<pre style="margin: 0;">-<span id="LC1914" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1915
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<pre style="margin: 0;">-<span id="LC1915" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1916
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<pre style="margin: 0;">-<span id="LC1916" class="line" lang="mosel"><span class="s1" style="color: #d14;">February 1995 </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1917
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<pre style="margin: 0;">-<span id="LC1917" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 1.0 (IMEG, PennState)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1918
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<pre style="margin: 0;">-<span id="LC1918" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1919
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<pre style="margin: 0;">-<span id="LC1919" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This is the first official version of paml. Three main programs are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1920
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<pre style="margin: 0;">-<span id="LC1920" class="line" lang="mosel"><span class="s1" style="color: #d14;"> included: baseml, basemlg and codeml. Control files are used for all</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1921
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1921" class="line" lang="mosel"><span class="s1" style="color: #d14;"> of them. The program codeml is formed by merging two programs codonml</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1922
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<pre style="margin: 0;">-<span id="LC1922" class="line" lang="mosel"><span class="s1" style="color: #d14;"> and aaml, for codon sequences and amino acid sequences, respectively.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1923
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<pre style="margin: 0;">-<span id="LC1923" class="line" lang="mosel"><span class="s1" style="color: #d14;"> One rate, gamma rates, and auto-discrete-gamma rates for sites are</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1924
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<pre style="margin: 0;">-<span id="LC1924" class="line" lang="mosel"><span class="s1" style="color: #d14;"> implemented for nucleotide, amino acid, and codon-based models. The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1925
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<pre style="margin: 0;">-<span id="LC1925" class="line" lang="mosel"><span class="s1" style="color: #d14;"> document is provided as postscript files (paml1_3.ps).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1926
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<pre style="margin: 0;">-<span id="LC1926" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1927
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<pre style="margin: 0;">-<span id="LC1927" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1928
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<pre style="margin: 0;">-<span id="LC1928" class="line" lang="mosel"><span class="s1" style="color: #d14;">October 1994 </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1929
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<pre style="margin: 0;">-<span id="LC1929" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 0.12, no name for package (BAU and IMEG PennState) </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1930
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<pre style="margin: 0;">-<span id="LC1930" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1931
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<pre style="margin: 0;">-<span id="LC1931" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The bracket notation of tree topologies is introduced. Tree</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1932
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<pre style="margin: 0;">-<span id="LC1932" class="line" lang="mosel"><span class="s1" style="color: #d14;"> search by star decomposition is implemented in baseml and codonml.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1933
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<pre style="margin: 0;">-<span id="LC1933" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The options for baseml are moved into an option file baseml.ctl. The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1934
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<pre style="margin: 0;">-<span id="LC1934" class="line" lang="mosel"><span class="s1" style="color: #d14;"> molecular clock seems to work with the automatic tree search model</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1935
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<pre style="margin: 0;">-<span id="LC1935" class="line" lang="mosel"><span class="s1" style="color: #d14;"> (runmode=1 or 2). The old readme file is renamed manual.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1936
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<pre style="margin: 0;">-<span id="LC1936" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1937
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<pre style="margin: 0;">-<span id="LC1937" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1938
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<pre style="margin: 0;">-<span id="LC1938" class="line" lang="mosel"><span class="s1" style="color: #d14;">March 1994 </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1939
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<pre style="margin: 0;">-<span id="LC1939" class="line" lang="mosel"><span class="s1" style="color: #d14;">Version 0.10, no name for package: (NHM, England)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1940
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<pre style="margin: 0;">-<span id="LC1940" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1941
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<pre style="margin: 0;">-<span id="LC1941" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Programs tripml and comptree are renamed codonml and rell. The readme</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1942
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<pre style="margin: 0;">-<span id="LC1942" class="line" lang="mosel"><span class="s1" style="color: #d14;"> file is expanded and the numerical optimization routine, ming1, used</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1943
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<pre style="margin: 0;">-<span id="LC1943" class="line" lang="mosel"><span class="s1" style="color: #d14;"> by dnaml and codonml, is improved. The discrete-gamma model of Yang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1944
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<pre style="margin: 0;">-<span id="LC1944" class="line" lang="mosel"><span class="s1" style="color: #d14;"> (1994 JME) is implemented in both baseml and codonml.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1945
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<pre style="margin: 0;">-<span id="LC1945" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1946
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<pre style="margin: 0;">-<span id="LC1946" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Preliminary version 0.11, no name for package: April 1994 (NHM,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1947
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<pre style="margin: 0;">-<span id="LC1947" class="line" lang="mosel"><span class="s1" style="color: #d14;"> England) Programs dnaml and dnamls are renamed baseml and basemlg to</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1948
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<pre style="margin: 0;">-<span id="LC1948" class="line" lang="mosel"><span class="s1" style="color: #d14;"> avoid confusion with Joe Felsenstein'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">programs</span><span class="p">.</span> <span class="n" style="color: #333;">The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1949
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<pre style="margin: 0;">-<span id="LC1949" class="line" lang="mosel"> <span class="n" style="color: #333;">auto</span><span class="p">-</span><span class="n" style="color: #333;">discrete</span><span class="p">-</span><span class="n" style="color: #333;">gamma</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">nonparametric</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">rate</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1950
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<pre style="margin: 0;">-<span id="LC1950" class="line" lang="mosel"> <span class="n" style="color: #333;">variation</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">correlation</span> <span class="n" style="color: #333;">mong</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="p">(</span><span class="m" style="color: #099;">1995</span> <span class="n" style="color: #333;">Genetics</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">added</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1951
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<pre style="margin: 0;">-<span id="LC1951" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">baseml</span><span class="p">.</span> <span class="n" style="color: #333;">Nonhomogeneous</span><span class="p">-</span><span class="n" style="color: #333;">process</span> <span class="n" style="color: #333;">models</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Roberts</span> <span class="p">(</span><span class="m" style="color: #099;">1995</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1952
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<pre style="margin: 0;">-<span id="LC1952" class="line" lang="mosel"> <span class="n" style="color: #333;">MBE</span><span class="p">)</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">implemented</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">baseml</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1953
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<pre style="margin: 0;">-<span id="LC1953" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1954
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<pre style="margin: 0;">-<span id="LC1954" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1955
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<pre style="margin: 0;">-<span id="LC1955" class="line" lang="mosel"><span class="n" style="color: #333;">April</span> <span class="m" style="color: #099;">1993</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1956
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1956" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span> <span class="m" style="color: #099;">0.01</span><span class="p">,</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">for</span> <span class="k" style="font-weight: 600;">package</span> <span class="p">(</span><span class="n" style="color: #333;">Cambridge</span><span class="p">).</span> <span class="n" style="color: #333;">Three</span> <span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1957
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1957" class="line" lang="mosel"><span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">package</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1958
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1958" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1959
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<pre style="margin: 0;">-<span id="LC1959" class="line" lang="mosel"> <span class="m" style="color: #099;">1.</span> <span class="n" style="color: #333;">dnamls</span> <span class="n" style="color: #333;">implements</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">gamma</span> <span class="n" style="color: #333;">rates</span> <span class="n" style="color: #333;">among</span> <span class="n" style="color: #333;">sites</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Yang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1960
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<pre style="margin: 0;">-<span id="LC1960" class="line" lang="mosel"> <span class="p">(</span><span class="m" style="color: #099;">1993</span><span class="p">)</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">works</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">arbitrary</span> <span class="n" style="color: #333;">topologies</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">substitution</span> <span class="n" style="color: #333;">models</span></span>
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1961
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<pre style="margin: 0;">-<span id="LC1961" class="line" lang="mosel"> <span class="p">(</span><span class="n" style="color: #333;">JC69</span><span class="p">,</span> <span class="n" style="color: #333;">K80</span><span class="p">,</span> <span class="n" style="color: #333;">F81</span><span class="p">,</span> <span class="n" style="color: #333;">HKY85</span><span class="p">).</span></span>
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1962
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<pre style="margin: 0;">-<span id="LC1962" class="line" lang="mosel"></span>
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1963
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<pre style="margin: 0;">-<span id="LC1963" class="line" lang="mosel"> <span class="m" style="color: #099;">2.</span> <span class="n" style="color: #333;">dnaml</span> <span class="n" style="color: #333;">implements</span> <span class="n" style="color: #333;">the</span> <span class="k" style="font-weight: 600;">model</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">rate</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">sites</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">The</span></span>
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1964
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<pre style="margin: 0;">-<span id="LC1964" class="line" lang="mosel"> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">Joe</span> <span class="n" style="color: #333;">Felsenstein</span><span class="s1" style="color: #d14;">'s program was used.)</span></span>
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1965
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<pre style="margin: 0;">-<span id="LC1965" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1966
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<pre style="margin: 0;">-<span id="LC1966" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 3. tripml implements the codon-based model of Goldman and Yang (1994).</span></span>
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1967
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<pre style="margin: 0;">-<span id="LC1967" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Trees are represented by the "branch notation".</span></span>
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1968
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<pre style="margin: 0;">-<span id="LC1968" class="line" lang="mosel"><span class="s1" style="color: #d14;"></span></span>
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1969
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<pre style="margin: 0;">-<span id="LC1969" class="line" lang="mosel"><span class="s1" style="color: #d14;">// end of file</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -272,7 +272,7 @@ int main(int argc, char *argv[])</td>
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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273
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Node %3d: %3s ( "</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fossils</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]);</span></span>
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274
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">npfossils</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%<span class="idiff left right">6</span>.4f"</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pfossil</span><span class="p">[</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UPPER_F</span><span class="p">)]);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%<span class="idiff left right">7</span>.4f"</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pfossil</span><span class="p">[</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UPPER_F</span><span class="p">)]);</span></span>
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276
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">npfossils</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" )</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">", "</span><span class="p">));</span></span>
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277
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="p">}</span></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1038,7 +1038,7 @@ int GetOptions(char *ctlf)</td>
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="c"><span class="p">{</span></span>
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1039
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">transform0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ARCSIN_B</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* default transform: SQRT_B, LOG_B, ARCSIN_B */</span></span>
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1040
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iopt</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">nopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">31</span><span class="p">,</span> <span class="n" style="color: #333;">lline</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4096</span><span class="p">;</span></span>
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1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">4096</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pline</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">peq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">opt</span><span class="p">[</span><span class="mi" style="color: #099;">33</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*#"</span><span class="p">;</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">4096</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pline</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">[</span><span class="mi" style="color: #099;">33</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*#"</span><span class="p">;</span></span>
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1042
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">optstr</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">"seed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"seqfile"</span><span class="p">,</span><span class="s" style="color: #d14;">"treefile"</span><span class="p">,</span> <span class="s" style="color: #d14;">"outfile"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mcmcfile"</span><span class="p">,</span> <span class="s" style="color: #d14;">"BayesFactorBeta"</span><span class="p">,</span></span>
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1043
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="c"> <span class="s" style="color: #d14;">"seqtype"</span><span class="p">,</span> <span class="s" style="color: #d14;">"aaRatefile"</span><span class="p">,</span> <span class="s" style="color: #d14;">"icode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"noisy"</span><span class="p">,</span> <span class="s" style="color: #d14;">"usedata"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ndata"</span><span class="p">,</span> <span class="s" style="color: #d14;">"duplication"</span><span class="p">,</span> <span class="s" style="color: #d14;">"model"</span><span class="p">,</span> <span class="s" style="color: #d14;">"clock"</span><span class="p">,</span></span>
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="c"> <span class="s" style="color: #d14;">"TipDate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"RootAge"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fossilerror"</span><span class="p">,</span> <span class="s" style="color: #d14;">"alpha"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ncatG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cleandata"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1595,128 +1595,213 @@ double Infinitesites(FILE *fout)</td>
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<pre style="margin: 0;"> <span id="LC1595" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">GetInitialsTimes</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="c"><span class="p">{</span></span>
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1598
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<pre style="margin: 0;">-<span id="LC1598" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* This sets calibration node ages and root age first, and then populates other node ages, by</span></span>
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<pre style="margin: 0;">-<span id="LC1599" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> a break-stick strategy.</span></span>
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1600
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<pre style="margin: 0;">-<span id="LC1600" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> It ensures that each node age is younger than its parent's age, but does not check </span></span>
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1601
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<pre style="margin: 0;">-<span id="LC1601" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> the consistency of ages against the fossil constraints. The use of soft bounds means that </span></span>
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1602
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<pre style="margin: 0;">-<span id="LC1602" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> any ages are possible, even if the chain may start from a poor place.</span></span>
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1603
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<pre style="margin: 0;">-<span id="LC1603" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> In the case of shared/mirrored node ages due to gene duplication, it is not so clear whether </span></span>
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1604
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<pre style="margin: 0;">-<span id="LC1604" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> conflicts may still arise.</span></span>
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<pre style="margin: 0;">-<span id="LC1605" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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1606
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<pre style="margin: 0;">-<span id="LC1606" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">k1</span><span class="p">,</span> <span class="n" style="color: #333;">ir</span><span class="p">,</span> <span class="n" style="color: #333;">ncorrections</span><span class="p">,</span> <span class="n" style="color: #333;">driver</span><span class="p">;</span></span>
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1607
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<pre style="margin: 0;">-<span id="LC1607" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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1608
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<pre style="margin: 0;">-<span id="LC1608" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">agefrom</span><span class="p">,</span> <span class="n" style="color: #333;">ageto</span><span class="p">;</span></span>
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1598
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<pre style="margin: 0;">+<span id="LC1598" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* This sets ages for nodes with bounds first. Then it goes through a loop looking for nodes </span></span>
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1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> with the largest min calibration, and another loop looking for the longest path, each </span></span>
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1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> case populating node ages on the path until reaching an ancestral node with assigned age or </span></span>
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1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> with max bound.</span></span>
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1602
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> In the case of shared/mirrored node ages due to gene duplication, conflicts may still arise,</span></span>
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1603
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> so that a loop of corrections is used.</span></span>
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1604
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="c"></span>
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1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> stree.duplication:</span></span>
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1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> stree.nodes[i].label = 0: usual node, which may and may not have calibration.</span></span>
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1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> stree.nodes[j].label =-1: node i is the driver node, whose age is shared by other nodes.</span></span>
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1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> It may and may not have calibration.</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> stree.nodes[j].label = i: node j shares the age of node i, and doesn't have calibration.</span></span>
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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span><span class="p">,</span> <span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">;</span></span>
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1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">k1</span><span class="p">,</span> <span class="n" style="color: #333;">ir</span><span class="p">,</span> <span class="n" style="color: #333;">ncorrections</span><span class="p">,</span> <span class="n" style="color: #333;">driver</span><span class="p">,</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">maxdepth</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmin</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmax</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pptable</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1609
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="c"></span>
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1610
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<td class="diff-line-num new_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BOUND_F</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1611
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<td class="diff-line-num new_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="c"> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">TipDate model requires bounds on the root age..</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1612
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<td class="diff-line-num new_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="c"></span>
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1613
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<td class="diff-line-num new_line old" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1613" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set up ages of calibration nodes */</span></span>
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1614
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<td class="diff-line-num new_line old" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1614" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> </span>
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1615
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<pre style="margin: 0;">-<span id="LC1615" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1616
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<td class="diff-line-num new_line old" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1616" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1617
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<pre style="margin: 0;">-<span id="LC1617" class="line" lang="c"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pfossil</span><span class="p">;</span></span>
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1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set up pop-pop table of ancestor-descendent relationships. */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="c"> <span class="n" style="color: #333;">pptable</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s21</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1622
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<pre style="margin: 0;">+<span id="LC1622" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pptable</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"oom pptable"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1623
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pptable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s21</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">pptable</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">s21</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="c"> <span class="n" style="color: #333;">tmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmin</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"oom tmin"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1627
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">tmin</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="c"> <span class="n" style="color: #333;">tmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="c"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"oom r"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<td class="diff-line-num new_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1619
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1619" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1620
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1620" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">LOWER_F</span><span class="p">):</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">05</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1621
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1621" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">UPPER_F</span><span class="p">):</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1622
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1622" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">BOUND_F</span><span class="p">):</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rndu</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">6</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1623
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1623" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">GAMMA_F</span><span class="p">):</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">7</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rndu</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">6</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1624
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1624" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">SKEWN_F</span><span class="p">):</span> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span><span class="n" style="color: #333;">SKEWT_F</span><span class="p">):</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1625
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1625" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1626
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1626" class="line" lang="c"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Pi</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1627
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1627" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">());</span></span>
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1628
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<pre style="margin: 0;">-<span id="LC1628" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1629
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<pre style="margin: 0;">-<span id="LC1629" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">S2N_F</span><span class="p">):</span> </span>
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1630
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<pre style="margin: 0;">-<span id="LC1630" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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1631
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1631" class="line" lang="c"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Pi</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* mean of SN 1 */</span></span>
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1632
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1632" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]);</span></span>
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1633
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1633" class="line" lang="c"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Pi</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* mean of SN 2 */</span></span>
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1634
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<td class="diff-line-num new_line old" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1634" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">());</span></span>
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1635
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<pre style="margin: 0;">-<span id="LC1635" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1632
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">root</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">root</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1635
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<pre style="margin: 0;">+<span id="LC1635" class="line" lang="c"> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="c"> <span class="p">}</span></span>
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1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* -1 means driver */</span></span>
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<pre style="margin: 0;">+<span id="LC1639" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* if j mirrors i, ancestors of j are also ancestors of i. */</span></span>
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">)</span> <span class="p">{</span></span>
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1642
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<pre style="margin: 0;">+<span id="LC1642" class="line" lang="c"> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1637" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC1638" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* copy nodes[i].age to all mirrored nodes */</span></span>
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1639
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<pre style="margin: 0;">-<span id="LC1639" class="line" lang="c"> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC1640" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">driver</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1641" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1642" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC1643" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1645" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* if j mirrors i, copy ancestors of i to j */</span></span>
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<pre style="margin: 0;">+<span id="LC1646" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">pptable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">pptable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1649
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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="c"> <span class="p">}</span></span>
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1650
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<pre style="margin: 0;">+<span id="LC1650" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1651
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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1652
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<pre style="margin: 0;">+<span id="LC1652" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Setting up initial node ages...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">pop-pop table:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> "</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1653
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<pre style="margin: 0;">+<span id="LC1653" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" %2d"</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1654
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<pre style="margin: 0;">+<span id="LC1654" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1655
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<pre style="margin: 0;">+<span id="LC1655" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%2d: "</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1656
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<pre style="margin: 0;">+<span id="LC1656" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" %2d"</span><span class="p">,</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1657
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" %3s "</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">fossils</span><span class="p">[</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1659
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<pre style="margin: 0;">+<span id="LC1659" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" label = %2d, "</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1660
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<pre style="margin: 0;">+<span id="LC1660" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"driver"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1661
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<pre style="margin: 0;">+<span id="LC1661" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"mirror"</span><span class="p">);</span></span>
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1644
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<td class="diff-line-num new_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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1645
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<td class="diff-line-num new_line" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1646
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<td class="diff-line-num new_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="c"> <span class="p">}</span></span>
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1647
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1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="c"></span>
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1648
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<pre style="margin: 0;">-<span id="LC1648" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check for consistency among calibration and mirrored nodes, and correct if needed. */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1649
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1649" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1650
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1650" class="line" lang="c"> <span class="n" style="color: #333;">ncorrections</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1651
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1651" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1652
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1652" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1653
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1653" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j is calibration node ancestral to i. */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1654
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1654" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">)</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1655
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1655" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1656
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1656" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1657
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1657" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">001</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">01</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1658
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1658" class="line" lang="c"> <span class="n" style="color: #333;">ncorrections</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1659
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1659" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* copy nodes[j].age to all mirrored nodes */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1660
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1660" class="line" lang="c"> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1661
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1661" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">driver</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1662
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1662" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1663
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<td class="diff-line-num new_line old" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1663" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1664
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<pre style="margin: 0;">-<span id="LC1664" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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1665
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<pre style="margin: 0;">-<span id="LC1665" class="line" lang="c"> <span class="p">}</span></span>
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1666
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<pre style="margin: 0;">-<span id="LC1666" class="line" lang="c"> <span class="p">}</span></span>
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1666
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<pre style="margin: 0;">+<span id="LC1666" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* retrieve tmin & rmax from calibrations */</span></span>
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1667
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<pre style="margin: 0;">+<span id="LC1667" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1668
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1670
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<pre style="margin: 0;">+<span id="LC1670" class="line" lang="c"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pfossil</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1671
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="c"></span>
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1672
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<pre style="margin: 0;">+<span id="LC1672" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1673
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<pre style="margin: 0;">+<span id="LC1673" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">LOWER_F</span><span class="p">):</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">UPPER_F</span><span class="p">):</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">BOUND_F</span><span class="p">):</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">GAMMA_F</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1677
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<pre style="margin: 0;">+<span id="LC1677" class="line" lang="c"> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QuantileGamma</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">025</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QuantileGamma</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">975</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1678
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<pre style="margin: 0;">+<span id="LC1678" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1679
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">SKEWN_F</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1680
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<pre style="margin: 0;">+<span id="LC1680" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">SKEWT_F</span><span class="p">):</span></span>
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1681
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<pre style="margin: 0;">+<span id="LC1681" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">S2N_F</span><span class="p">):</span></span>
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1682
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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="c"> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"implement SkewN, Skewt, S2N now"</span><span class="p">);</span></span>
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1683
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="c"> <span class="p">}</span></span>
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1684
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<pre style="margin: 0;">+<span id="LC1684" class="line" lang="c"> <span class="p">}</span></span>
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1685
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1686
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<pre style="margin: 0;">+<span id="LC1686" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1687
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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="p">{</span></span>
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1688
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">daughter node %3d minimun age %9.4f </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">mother node %3d max age %9.4f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1689
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="c"> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"strange calibration?"</span><span class="p">);</span></span>
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1690
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<pre style="margin: 0;">+<span id="LC1690" class="line" lang="c"> <span class="p">}</span></span>
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1691
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<pre style="margin: 0;">+<span id="LC1691" class="line" lang="c"> <span class="p">}</span></span>
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1692
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<pre style="margin: 0;">+<span id="LC1692" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1693
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="cm" style="color: #998; font-style: italic;">/* remove duplicated min bounds for ancestors of i */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1695
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1696
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<pre style="margin: 0;">+<span id="LC1696" class="line" lang="c"> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="cm" style="color: #998; font-style: italic;">/* remove duplicated max bounds for descendents of i */</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pptable</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s21</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="c"> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1667
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1701
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<pre style="margin: 0;"> <span id="LC1701" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">bounds on nodes after removing duplicated min and max bounds"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%2d: (%8.4f, %8.4f)"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1668
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<td class="diff-line-num new_line" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="c"> <span class="p">}</span></span>
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1669
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<td class="diff-line-num new_line old" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1669" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ncorrections</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1670
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<td class="diff-line-num new_line" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1709
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="c"> <span class="p">}</span></span>
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1671
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<td class="diff-line-num new_line old" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1671" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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1672
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<td class="diff-line-num new_line old" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1672" class="line" lang="c"> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"i did 100 rounds, but we need more!"</span><span class="p">);</span></span>
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1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* generate ages for bounded nodes if possible. */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1712
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1713
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">root</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"we need a maximum-age bound on root??"</span><span class="p">);</span></span>
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1673
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1716
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<pre style="margin: 0;"> <span id="LC1716" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1674
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<td class="diff-line-num new_line old" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1674" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* look for the deepest path from a node to its ancestor, and assign ages to all nodes inbetween. */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1675
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<td class="diff-line-num new_line old" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1675" class="line" lang="c"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1676
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<td class="diff-line-num new_line old" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1676" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"oom r"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1717
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<pre style="margin: 0;">+<span id="LC1717" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* look for largest unused tmin, and assign ages on path from node to ancestor with age or with tmax. */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1718
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1719
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<pre style="margin: 0;">+<span id="LC1719" class="line" lang="c"> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1720
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* find max tmin and store in tbpath[0]. */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1721
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<pre style="margin: 0;">+<span id="LC1721" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="c"> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmin</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1723
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<pre style="margin: 0;">+<span id="LC1723" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1724
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<pre style="margin: 0;">+<span id="LC1724" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="c"> <span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1727
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">maxdepth</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1729
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1730
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="c"> <span class="n" style="color: #333;">maxdepth</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1735
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="c"> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1736
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="c"> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1677
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<td class="diff-line-num new_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1737
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<pre style="margin: 0;"> <span id="LC1737" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1678
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1678" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1679
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1679" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1680
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1680" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1681
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1681" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1682
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1682" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1683
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1683" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1684
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<td class="diff-line-num new_line old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1684" class="line" lang="c"> <span class="n" style="color: #333;">depth</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1738
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxdepth</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rndu</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1739
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxdepth</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">maxdepth</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">),</span> <span class="n" style="color: #333;">comparedouble</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">maxdepth</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1742
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="c"> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">driver</span><span class="p">)</span> <span class="p">{</span></span>
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1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">k1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k1</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span><span class="p">))</span></span>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k1</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="c"> <span class="p">}</span></span>
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1748
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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="c"> <span class="p">}</span></span>
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1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="c"> <span class="p">}</span></span>
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1750
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">*** min-age round %2d: from nodes %3d (%9.5f) to %3d, %3d nodes "</span><span class="p">,</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">maxdepth</span><span class="p">);</span></span>
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1751
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<pre style="margin: 0;">+<span id="LC1751" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">200</span><span class="p">)</span> <span class="n" style="color: #333;">printStree</span><span class="p">();</span></span>
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1752
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<pre style="margin: 0;">+<span id="LC1752" class="line" lang="c"> <span class="p">}</span></span>
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1753
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="c"></span>
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1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* look for longest path, and assign ages on path from node to ancestor with age or with tmax. */</span></span>
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1755
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<pre style="margin: 0;">+<span id="LC1755" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1756" class="line" lang="c"> <span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1757
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s21</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1759
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1760
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="1761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1761
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<pre style="margin: 0;">+<span id="LC1761" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1762
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="c"> <span class="n" style="color: #333;">depth</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1765
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="c"> <span class="p">}</span></span>
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1685
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<td class="diff-line-num new_line" data-linenumber="1766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1766
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<pre style="margin: 0;"> <span id="LC1766" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1686
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<td class="diff-line-num new_line" data-linenumber="1767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1767
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<pre style="margin: 0;"> <span id="LC1767" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">depth</span><span class="p">)</span> <span class="p">{</span></span>
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1687
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<td class="diff-line-num new_line" data-linenumber="1768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1768
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<pre style="margin: 0;"> <span id="LC1768" class="line" lang="c"> <span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1688
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1769
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<pre style="margin: 0;"> <span id="LC1769" class="line" lang="c"> <span class="p">}</span></span>
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1689
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<td class="diff-line-num new_line" data-linenumber="1770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1770
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<pre style="margin: 0;"> <span id="LC1770" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1690
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<td class="diff-line-num new_line" data-linenumber="1771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1771
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<pre style="margin: 0;"> <span id="LC1771" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* all ages are assigned. */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1772
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<pre style="margin: 0;">+<span id="LC1772" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1773
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<pre style="margin: 0;">+<span id="LC1773" class="line" lang="c"> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max2</span><span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]].</span><span class="n" style="color: #333;">age</span><span class="p">);</span></span>
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1774
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<pre style="margin: 0;">+<span id="LC1774" class="line" lang="c"> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tmax</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1775
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<pre style="margin: 0;">+<span id="LC1775" class="line" lang="c"></span>
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1691
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<td class="diff-line-num new_line" data-linenumber="1776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1776
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<pre style="margin: 0;"> <span id="LC1776" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxdepth</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rndu</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1692
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<td class="diff-line-num new_line old" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1692" class="line" lang="c"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">maxdepth</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">),</span> <span class="n" style="color: #333;">comparedouble</span><span class="p">);</span></span>
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1693
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<td class="diff-line-num new_line old" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1693" class="line" lang="c"> <span class="n" style="color: #333;">agefrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1694
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<td class="diff-line-num new_line old" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1694" class="line" lang="c"> <span class="n" style="color: #333;">ageto</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">to</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1695
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<td class="diff-line-num new_line old" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1695" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">to</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1696
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<td class="diff-line-num new_line old" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1696" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agefrom</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">ageto</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">agefrom</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">maxdepth</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">maxdepth</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">),</span> <span class="n" style="color: #333;">comparedouble</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1778
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">maxdepth</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1779
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<pre style="margin: 0;">+<span id="LC1779" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tbpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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1697
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<td class="diff-line-num new_line" data-linenumber="1780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1780
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="c"> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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1698
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<td class="diff-line-num new_line" data-linenumber="1781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">driver</span><span class="p">)</span> <span class="p">{</span></span>
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1699
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<td class="diff-line-num new_line old" data-linenumber="1782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1699" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1782
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<pre style="margin: 0;">+<span id="LC1782" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s<span class="idiff left right">2</span>1</span><span class="p">;</span> <span class="n" style="color: #333;">k1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1700
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<td class="diff-line-num new_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1783
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<pre style="margin: 0;"> <span id="LC1783" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">k1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k1</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1701
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<td class="diff-line-num new_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k1</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1702
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<td class="diff-line-num new_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1785
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1703
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<td class="diff-line-num new_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1786
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<pre style="margin: 0;"> <span id="LC1786" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1704
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<td class="diff-line-num new_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1788
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">*** longest-path round %2d: from nodes %3d (%9.5f) to %3d, %3d nodes "</span><span class="p">,</span> <span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">maxdepth</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1789
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">200</span><span class="p">)</span> <span class="n" style="color: #333;">printStree</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1705
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<td class="diff-line-num new_line" data-linenumber="1790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1790
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1706
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<td class="diff-line-num new_line" data-linenumber="1791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1707
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<td class="diff-line-num new_line old" data-linenumber="1792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1707" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1708
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<td class="diff-line-num new_line" data-linenumber="1792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1792
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<pre style="margin: 0;"> <span id="LC1792" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check for consistency for all nodes, and correct if needed. */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1709
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<td class="diff-line-num new_line" data-linenumber="1793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1793
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1710
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<td class="diff-line-num new_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="c"> <span class="n" style="color: #333;">ncorrections</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1711
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<td class="diff-line-num new_line old" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1711" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1795
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<pre style="margin: 0;">+<span id="LC1795" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s<span class="idiff left right">2</span>1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1712
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<td class="diff-line-num new_line" data-linenumber="1796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1796
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">father</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1713
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<td class="diff-line-num new_line" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1797
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<pre style="margin: 0;"> <span id="LC1797" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1798
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">*** correction round %2d nodes %2d & %2d, ages %9.5f %9.5f"</span><span class="p">,</span> <span class="n" style="color: #333;">ir</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1714
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<td class="diff-line-num new_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="c"> <span class="n" style="color: #333;">ncorrections</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1715
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<td class="diff-line-num new_line" data-linenumber="1800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mo" style="color: #099;">001</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">01</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1716
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<td class="diff-line-num new_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* copy nodes[j].age to all mirrored nodes */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1717
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<td class="diff-line-num new_line" data-linenumber="1802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="c"> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1718
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<td class="diff-line-num new_line" data-linenumber="1803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">driver</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1719
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<td class="diff-line-num new_line old" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1719" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1804
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<pre style="margin: 0;">+<span id="LC1804" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s<span class="idiff left right">2</span>1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1720
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<td class="diff-line-num new_line" data-linenumber="1805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1805
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<pre style="margin: 0;"> <span id="LC1805" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">driver</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1721
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<td class="diff-line-num new_line" data-linenumber="1806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1806
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<pre style="margin: 0;"> <span id="LC1806" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1722
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<td class="diff-line-num new_line" data-linenumber="1807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1807
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<pre style="margin: 0;"> <span id="LC1807" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1724,10 +1809,8 @@ int GetInitialsTimes(void)</td>
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1724
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1809
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<pre style="margin: 0;"> <span id="LC1809" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1725
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<td class="diff-line-num new_line" data-linenumber="1810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1810
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<pre style="margin: 0;"> <span id="LC1810" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ncorrections</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1726
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<td class="diff-line-num new_line" data-linenumber="1811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1811
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<pre style="margin: 0;"> <span id="LC1811" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1727
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<td class="diff-line-num new_line old" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1727" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ir</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1728
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<td class="diff-line-num new_line old" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1728" class="line" lang="c"> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"i did 100 rounds, but we need more!"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1729
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<td class="diff-line-num new_line" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1812
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<pre style="margin: 0;"> <span id="LC1812" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1730
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<pre style="margin: 0;">-<span id="LC1730" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1813
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<pre style="margin: 0;">+<span id="LC1813" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">pptable</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">free</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmin</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">free</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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1731
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1814
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<pre style="margin: 0;"> <span id="LC1814" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1732
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<td class="diff-line-num new_line" data-linenumber="1815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1815
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<pre style="margin: 0;"> <span id="LC1815" class="line" lang="c"><span class="p">}</span></span>
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1733
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1816
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3808,14 +3891,14 @@ int DescriptiveStatisticsSimpleMCMCTREE(FILE *fout, char infile[], int nbin)</td>
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3808
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3891
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<pre style="margin: 0;"> <span id="LC3891" class="line" lang="c"> <span class="p">}</span></span>
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3809
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<td class="diff-line-num new_line" data-linenumber="3892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3892
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<pre style="margin: 0;"> <span id="LC3892" class="line" lang="c"> <span class="p">}</span></span>
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3810
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<td class="diff-line-num new_line" data-linenumber="3893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3893
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<pre style="margin: 0;"> <span id="LC3893" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3811
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<td class="diff-line-num new_line old" data-linenumber="3894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3811" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Posterior mean (95%% Equal-tail CI) (95%% HPD CI) HPD-CI-width</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3894
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<pre style="margin: 0;">+<span id="LC3894" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Posterior mean<span class="idiff left right">s</span> (95%% Equal-tail CI) (95%% HPD CI) HPD-CI-width</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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3812
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<td class="diff-line-num new_line" data-linenumber="3895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3895
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<pre style="margin: 0;"> <span id="LC3895" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SkipC1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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3813
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<td class="diff-line-num new_line" data-linenumber="3896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3896
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<pre style="margin: 0;"> <span id="LC3896" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%-10s "</span><span class="p">,</span> <span class="n" style="color: #333;">varstr</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3814
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<td class="diff-line-num new_line old" data-linenumber="3897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3814" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%10.4f (%<span class="idiff left right">6.4f, %6.4f) (%6.4f, %6.4f) %6</span>.4f"</span><span class="p">,</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3897
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<pre style="margin: 0;">+<span id="LC3897" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%10.4f (%<span class="idiff left right">7.4f, %7.4f) (%7.4f, %7.4f) %7</span>.4f"</span><span class="p">,</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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3815
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<td class="diff-line-num new_line" data-linenumber="3898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3898
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<pre style="margin: 0;"> <span id="LC3898" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">SkipC1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3816
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<td class="diff-line-num new_line" data-linenumber="3899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3899
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<pre style="margin: 0;"> <span id="LC3899" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" (Jnode %2d)"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SkipC1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="3817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3817
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<td class="diff-line-num new_line" data-linenumber="3900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3900
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<pre style="margin: 0;"> <span id="LC3900" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span><span class="p">)</span></span>
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3818
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<pre style="margin: 0;">-<span id="LC3818" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" time: %<span class="idiff left right">6.2f (%5.2f, %5.2</span>f)"</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3901
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<pre style="margin: 0;">+<span id="LC3901" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" time: %<span class="idiff left right">7.3f (%6.3f, %6.3</span>f)"</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">,</span></span>
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3819
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<td class="diff-line-num new_line" data-linenumber="3902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3902
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<pre style="margin: 0;"> <span id="LC3902" class="line" lang="c"> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">);</span></span>
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3820
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<td class="diff-line-num new_line" data-linenumber="3903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3903
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<pre style="margin: 0;"> <span id="LC3903" class="line" lang="c"> <span class="p">}</span></span>
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3821
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<td class="diff-line-num new_line" data-linenumber="3904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3904
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<pre style="margin: 0;"> <span id="LC3904" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3827,11 +3910,11 @@ int DescriptiveStatisticsSimpleMCMCTREE(FILE *fout, char infile[], int nbin)</td>
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3827
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<td class="diff-line-num new_line" data-linenumber="3910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3910
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<pre style="margin: 0;"> <span id="LC3910" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Posterior mean (95%% Equal-tail CI) (95%% HPD CI) HPD-CI-width</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="3828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3828
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<td class="diff-line-num new_line" data-linenumber="3911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3911
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<pre style="margin: 0;"> <span id="LC3911" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SkipC1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3829
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<td class="diff-line-num new_line" data-linenumber="3912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3912
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<pre style="margin: 0;"> <span id="LC3912" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s "</span><span class="p">,</span> <span class="n" style="color: #333;">varstr</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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3830
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<td class="diff-line-num new_line old" data-linenumber="3913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3830" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10.4f (%<span class="idiff left right">6.4f, %6.4f) (%6.4f, %6.4f) %6</span>.4f"</span><span class="p">,</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3913
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<pre style="margin: 0;">+<span id="LC3913" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10.4f (%<span class="idiff left right">7.4f, %7.4f) (%7.4f, %7.4f) %7</span>.4f"</span><span class="p">,</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">xHPD975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xHPD025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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3831
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<td class="diff-line-num new_line" data-linenumber="3914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3914
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<pre style="margin: 0;"> <span id="LC3914" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">SkipC1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3832
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<td class="diff-line-num new_line" data-linenumber="3915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3915
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<pre style="margin: 0;"> <span id="LC3915" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" (Jnode %2d)"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SkipC1</span><span class="p">);</span></span>
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3833
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<td class="diff-line-num new_line" data-linenumber="3916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3916
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<pre style="margin: 0;"> <span id="LC3916" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3834
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<td class="diff-line-num new_line old" data-linenumber="3917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3834" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" time: %<span class="idiff left right">6.2f (%5.2f, %5.2</span>f)"</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3917
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<pre style="margin: 0;">+<span id="LC3917" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" time: %<span class="idiff left right">7.3f (%6.3f, %6.3</span>f)"</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mean</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">,</span></span>
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3835
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<td class="diff-line-num new_line" data-linenumber="3918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3918
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<pre style="margin: 0;"> <span id="LC3918" class="line" lang="c"> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x975</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x025</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">TipDate_TimeUnit</span><span class="p">);</span></span>
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3836
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3919
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<pre style="margin: 0;"> <span id="LC3919" class="line" lang="c"> <span class="p">}</span></span>
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3837
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<td class="diff-line-num new_line" data-linenumber="3920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3920
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<pre style="margin: 0;"> <span id="LC3920" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3867,7 +3950,7 @@ int MCMC(FILE* fout)</td>
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3867
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3950
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<pre style="margin: 0;"> <span id="LC3950" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%d burnin, sampled every %d, %d samples</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3868
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<td class="diff-line-num new_line" data-linenumber="3951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3951
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<pre style="margin: 0;"> <span id="LC3951" class="line" lang="c"> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">burnin</span><span class="p">,</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">sampfreq</span><span class="p">,</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">nsample</span><span class="p">);</span></span>
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3869
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<td class="diff-line-num new_line" data-linenumber="3952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3952
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<pre style="margin: 0;"> <span id="LC3952" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">usedata</span><span class="p">)</span> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"Approximating posterior"</span><span class="p">);</span></span>
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3870
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<td class="diff-line-num new_line old" data-linenumber="3953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3870" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"Approximating prior"</span><span class="p">);</span></span>
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3953
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<pre style="margin: 0;">+<span id="LC3953" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"Approximating prior"</span><span class="p">);</span></span>
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3871
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3954
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<pre style="margin: 0;"> <span id="LC3954" class="line" lang="c"></span>
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3872
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<td class="diff-line-num new_line" data-linenumber="3955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3955
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<pre style="margin: 0;"> <span id="LC3955" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(Settings: cleandata=%d print=%d saveconP=%d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3873
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3956
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<pre style="margin: 0;"> <span id="LC3956" class="line" lang="c"> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">,</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">,</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">saveconP</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3877,9 +3960,10 @@ int MCMC(FILE* fout)</td>
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3877
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3960
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<pre style="margin: 0;"> <span id="LC3960" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">nsteplength</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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3878
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3961
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<pre style="margin: 0;"> <span id="LC3961" class="line" lang="c"> <span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">steplength</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">001</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rndu</span><span class="p">();</span></span>
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3879
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3962
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<pre style="margin: 0;"> <span id="LC3962" class="line" lang="c"></span>
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3963
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<pre style="margin: 0;">+<span id="LC3963" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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3880
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<td class="diff-line-num new_line" data-linenumber="3964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3964
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<pre style="margin: 0;"> <span id="LC3964" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> printf("\nsteplength values: ");</span></span>
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<td class="diff-line-num old_line" data-linenumber="3881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3881
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3965
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<pre style="margin: 0;"> <span id="LC3965" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> matout2(F0, mcmc.steplength, 1, mcmc.nsteplength, 9, 5);</span></span>
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3882
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<pre style="margin: 0;">-<span id="LC3882" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC3966" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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3967
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<pre style="margin: 0;"> <span id="LC3967" class="line" lang="c"> <span class="n" style="color: #333;">printStree</span><span class="p">();</span></span>
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3884
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3968
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<pre style="margin: 0;"> <span id="LC3968" class="line" lang="c"></span>
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3885
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3969
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<pre style="margin: 0;"> <span id="LC3969" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">np</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99#92dbb696e9045a01875b9f9494678f0dfc5a05cd"><strong>src/paml.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,14 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FOR(i,n) for(i=0; i<n; i++)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FPN(file) fputc('\n', file)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define F0 stdout</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if !defined(MAX)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX(a,b) (((a) > (b)) ? (a) : (b))</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if !defined(MIN)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN(a,b) (((a) < (b)) ? (a) : (b))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SQUARE(a) ((a)*(a))</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define min2(a,b) ((a)<(b)?(a):(b))</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define max2(a,b) ((a)>(b)?(a):(b))</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define swap2(a,b,y) { y=a; a=b; b=y; }</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -386,6 +394,6 @@ enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} Out</td>
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386
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="c"></span>
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387
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PAML_RELEASE 0</span></span>
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388
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define pamlVerStr "paml version 4.9<span class="idiff left right">i, September 2018</span>"</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define pamlVerStr "paml version 4.9<span class="idiff left right">j, October 2019</span>"</span></span>
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390
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"></span>
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391
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99#a285bdff300c2b5227532ac230a53690458860a1"><strong>src/pll_avx.c</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015 Tomas Flouri</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> published by the Free Software Foundation, either version 3 of the</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> License, or (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> GNU Affero General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU Affero General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Contact: Tomas Flouri <Tomas.Flouri@h-its.org>,</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Exelixis Lab, Heidelberg Instutute for Theoretical Studies</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_MSC_VER)</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">__declspec</span><span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">__declspec</span><span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">aligned</span> <span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">)));</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">aligned</span> <span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">)));</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pmat_jc69</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="p">{</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">0001</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">printf</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">t = %.5f in pijJC69"</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> </span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1e-100</span><span class="p">)</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="p">{</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="p">}</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="p">}</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_tip</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="p">{</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="p">{</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// for (i = 0; i < states; ++i)</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// clv[i] = lmat[i] * rmat[i];</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> </span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">_mm256_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">);</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="p">}</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"><span class="p">}</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_tip_amb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"><span class="p">{</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lvec</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rvec</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"> </span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="p">{</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> </span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nChara</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"> <span class="p">{</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="p">}</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nChara</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"> <span class="p">}</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm0</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">_mm256_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="p">}</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"><span class="p">}</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_inner</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"><span class="p">{</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> </span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">,</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="p">{</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">;</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c"></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="c"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c"></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute y */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">ymm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="c"></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_permute2f128_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span> <span class="n" style="color: #333;">_MM_SHUFFLE</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_blend_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute x*y */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">);</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c"></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c"> <span class="n" style="color: #333;">_mm256_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span> <span class="n" style="color: #333;">xmm0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c"></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_inner_amb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">,</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute term for left child (tip) */</span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nChara</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="p">}</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute term for right child (inner) */</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">ymm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c"></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_permute2f128_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span> <span class="n" style="color: #333;">_MM_SHUFFLE</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_blend_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">);</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">_mm256_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span><span class="n" style="color: #333;">ymm0</span><span class="p">);</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"> </span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c"><span class="p">}</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">inner_inner</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"><span class="p">{</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">,</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">;</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c"></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="c"> <span class="p">{</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span><span class="p">;</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute vector of x */</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lclv</span><span class="p">);</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c"></span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="c"></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute x */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="c"></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="c"></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_permute2f128_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span> <span class="n" style="color: #333;">_MM_SHUFFLE</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_blend_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c"></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute y */</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="c"></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="c"> <span class="n" style="color: #333;">ymm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpackhi_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_unpacklo_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_permute2f128_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span> <span class="n" style="color: #333;">_MM_SHUFFLE</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_blend_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="c"></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute x*y */</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">);</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="c"> <span class="n" style="color: #333;">_mm256_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span> <span class="n" style="color: #333;">xmm0</span><span class="p">);</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="c"></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="c"> <span class="n" style="color: #333;">lclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="c"> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="c"> <span class="p">}</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ConditonalPNode</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inode</span><span class="p">)</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="c"><span class="p">{</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="n" style="color: #333;">rchild</span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* recursive call the ConditionalPNode on all children of the current node */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">nson</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"> <span class="p">{</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get id of i-th child of current node */</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="c"> <span class="n" style="color: #333;">child</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* if child is an inner node then recursively compute its conditional</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> probabilities vector */</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">child</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">saveconP</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">oldconP</span><span class="p">[</span><span class="n" style="color: #333;">child</span><span class="p">]))</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">ConditonalPNode</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="c"> <span class="p">}</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize CLV entries of current node to 1 */</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="c"> <span class="n" style="color: #333;">lchild</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"> <span class="n" style="color: #333;">rchild</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ltip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rtip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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418
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="c"></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ltip</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rtip</span><span class="p">)</span></span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> <span class="p">{</span></span>
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421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">)</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"> <span class="n" style="color: #333;">tip_tip</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"> <span class="n" style="color: #333;">tip_tip_amb</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"> <span class="p">}</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ltip</span><span class="p">)</span></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">)</span></span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner_amb</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"> <span class="p">}</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rtip</span><span class="p">)</span></span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c"> <span class="p">{</span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">)</span></span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner</span><span class="p">(</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner_amb</span><span class="p">(</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="c"> <span class="p">}</span></span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="c"> <span class="n" style="color: #333;">inner_inner</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c"></span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="c"><span class="p">}</span></span></pre>
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<li id="6c4ed75b16bf498d6c4b6a1032a8793efc182652">
<a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99#6c4ed75b16bf498d6c4b6a1032a8793efc182652"><strong>src/pll_sse.c</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015 Tomas Flouri</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> published by the Free Software Foundation, either version 3 of the</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> License, or (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> GNU Affero General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU Affero General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Contact: Tomas Flouri <Tomas.Flouri@h-its.org>,</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Exelixis Lab, Heidelberg Instutute for Theoretical Studies</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_MSC_VER)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">__declspec</span><span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">__declspec</span><span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">aligned</span> <span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">aligned</span> <span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pmat_jc69</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">0001</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">printf</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">t = %.5f in pijJC69"</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> </span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1e-100</span><span class="p">)</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="p">}</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="p">{</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">pmatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="p">}</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_tip</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="p">{</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="p">{</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Vectorization of the following code snippet</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> (only applicable to JC69)</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for (i = 0; i < states; ++i)</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> clv[i] = lmat[i] * rmat[i];</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="p">}</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"><span class="p">}</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_tip_amb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"><span class="p">{</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lvec</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rvec</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"> </span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">;</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nChara</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"> <span class="p">}</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nChara</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">][</span><span class="n" style="color: #333;">n</span><span class="p">]][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">ymm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">);</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">ymm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="p">}</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm0</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm1</span><span class="p">);</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"> <span class="p">}</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"><span class="p">}</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_inner</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"><span class="p">{</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm5</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">,</span><span class="n" style="color: #333;">xmm9</span><span class="p">;</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Vectorization of the following code snippet</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for (j = 0; j < states; ++j)</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> {</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> y = 0;</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for (k = 0; k < states; ++k)</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> y += rmat[k] * rclv[k];</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> rmat += states;</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> clv[j] = y*lmat[j];</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c"></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b1*d1 + b2*d2 | b3*d3 + b4*d4) */</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (1) */</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c"></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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232
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"></span>
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233
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b5*d1 + b6*d2 | b7*d3 + b8*d4) */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (2) */</span></span>
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235
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c"></span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">);</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"></span>
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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b9*d1 + b10*d2 | b11*d3 + b12*d4) */</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm5</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (3) */</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="c"></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b13*d1 + b14*d2 | b15*d3 + b16*d4) */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (4) */</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
258
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b1*d1 + b2*d2 + b3*d3 + b4*d3 |</span></span>
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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> b5*d1 + b6*d2 + b7*d3 + b8*d4 ) */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b9*d1 + b10*d2 + b11*d3 + b12*d3 |</span></span>
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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> b13*d1 + b14*d2 + b15*d3 + b16*d4 ) */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">);</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"> <span class="p">}</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c"><span class="p">}</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tip_inner_amb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"><span class="p">{</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"></span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">ymm2</span><span class="p">,</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm5</span><span class="p">,</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">,</span><span class="n" style="color: #333;">ymm8</span><span class="p">,</span><span class="n" style="color: #333;">ymm9</span><span class="p">;</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c"></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute term for left child (tip) */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nChara</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">CharaMap</span><span class="p">[</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">][</span><span class="n" style="color: #333;">h</span><span class="p">]][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// *states;</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="c"> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="c"></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute term for right child (inner) */</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"> <span class="n" style="color: #333;">ymm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">ymm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">ymm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">ymm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b1*d1 + b2*d2 | b3*d3 + b4*d4) */</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm6</span><span class="p">,</span><span class="n" style="color: #333;">ymm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (2) */</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c"></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c"></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">ymm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c"> <span class="n" style="color: #333;">ymm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b5*d1 + b6*d2 | b7*d3 + b8*d4) */</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm8</span><span class="p">,</span><span class="n" style="color: #333;">ymm9</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (4) */</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm5</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="c"> <span class="n" style="color: #333;">ymm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">);</span></span>
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335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span> <span class="n" style="color: #333;">ymm9</span><span class="p">);</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="c"></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="c"> <span class="n" style="color: #333;">ymm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm6</span><span class="p">);</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c"></span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="c"> <span class="n" style="color: #333;">ymm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">ymm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm6</span><span class="p">);</span></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c"> </span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b9*d1 + b10*d2 | b11*d3 + b12*d4) */</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c"> <span class="n" style="color: #333;">ymm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm7</span><span class="p">,</span><span class="n" style="color: #333;">ymm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (2) */</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c"></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="c"> <span class="n" style="color: #333;">ymm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm3</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="c"> <span class="n" style="color: #333;">ymm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm4</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b13*d1 + b14*d2 | b15*d3 + b16*d4) */</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="c"> <span class="n" style="color: #333;">ymm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm8</span><span class="p">,</span><span class="n" style="color: #333;">ymm9</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (4) */</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">ymm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">ymm5</span><span class="p">,</span><span class="n" style="color: #333;">ymm7</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"> <span class="n" style="color: #333;">ymm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">ymm2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">ymm9</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">inner_inner</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchild</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">clv</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="c"></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">lmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"> <span class="n" style="color: #333;">pmat_jc69</span><span class="p">(</span><span class="n" style="color: #333;">rmatrix</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">branch</span><span class="p">);</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="c"></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">;</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="c"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">xmm5</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">,</span><span class="n" style="color: #333;">xmm9</span><span class="p">;</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="c"></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<td class="diff-line-num old old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +-----+-----+-----+-----+ +-----+-----+-----+-----+</span></span>
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<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
387
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> | a1 | a2 | a3 | a4 | | b1 | b2 | b3 | b4 |</span></span>
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<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +-----+-----+-----+-----+ +-----+-----+-----+-----+</span></span>
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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
389
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> | a5 | a6 | a7 | a8 | | b5 | b6 | b7 | b8 |</span></span>
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<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +-----+-----+-----+-----+ +-----+-----+-----+-----+</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
391
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> | a9 | a10 | a11 | a12 | | b9 | b10 | b11 | b12 |</span></span>
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<td class="diff-line-num old old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +-----+-----+-----+-----+ +-----+-----+-----+-----+</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
393
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> | a13 | a14 | a15 | a16 | | b13 | b14 | b15 | b16 |</span></span>
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<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +-----+-----+-----+-----+ +-----+-----+-----+-----+</span></span>
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<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x x</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +----+----+----+----+ +----+----+----+----+</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> | c1 | c2 | c3 | c4 | | d1 | d2 | d3 | d4 |</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> +----+----+----+----+ +----+----+----+----+</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sites</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> <span class="p">{</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lmatrix</span><span class="p">;</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rmatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c"></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Vectorization of the following code snippet</span></span>
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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for (j = 0; j < states; ++j)</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> {</span></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x = 0;</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> y = 0;</span></span>
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418
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for (k = 0; k < states; ++k)</span></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x += lmat[k] * lclv[k];</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> y += rmat[k] * rclv[k];</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> lmat += states;</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> rmat += states;</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> clv[j] = x*y;</span></span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"></span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute left */</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="c"> <span class="n" style="color: #333;">xmm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lclv</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="c"></span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lclv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="c"></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (a1*c1 + a2*c2 | a3*c3 + a4*c4) */</span></span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (1) */</span></span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="c"></span>
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444
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute right */</span></span>
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445
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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446
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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447
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm4</span><span class="p">);</span></span>
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448
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="c"></span>
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449
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="c"> <span class="n" style="color: #333;">xmm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rclv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed */</span></span>
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450
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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451
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="c"></span>
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453
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b1*d1 + b2*d2 | b3*d3 + b4*d4) */</span></span>
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454
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (2) */</span></span>
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455
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="c"></span>
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456
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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457
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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458
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="c"></span>
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459
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute left */</span></span>
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460
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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461
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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462
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
463
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
464
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="c"></span>
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466
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (a5*c1 + a6*c2 | a7*c3 + a8*c4) */</span></span>
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467
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm7</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (3) */</span></span>
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468
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="c"></span>
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469
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute right */</span></span>
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470
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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471
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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472
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="c"></span>
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473
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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474
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="c"> <span class="n" style="color: #333;">xmm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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475
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="c"> </span>
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476
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b5*d1 + b6*d2 | b7*d3 + b8*d4) */</span></span>
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477
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm8</span><span class="p">,</span><span class="n" style="color: #333;">xmm9</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (4) */</span></span>
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478
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="c"> </span>
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479
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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480
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm5</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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481
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;">xmm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm8</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="p">,</span> <span class="n" style="color: #333;">xmm9</span><span class="p">);</span></span>
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483
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="c"></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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486
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="c"></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute left */</span></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm5</span><span class="p">);</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="c"></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (a9*c1 + a10*c2 | a11*c3 + a12*c4) */</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm6</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (1) */</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="c"></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute right */</span></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="c"></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="c"> </span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b9*d1 + b10*d2 | b11*d3 + b12*d4) */</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="c"> <span class="n" style="color: #333;">xmm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm7</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (2) */</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="c"> </span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="c"> <span class="n" style="color: #333;">rmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="c"> <span class="n" style="color: #333;">lmat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="c"></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute left */</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="p">);</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm0</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="c"></span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">lmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="c"></span>
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517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (a13*c1 + a14*c2 | a15*c3 + a16*c4) */</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="c"> <span class="n" style="color: #333;">xmm6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm7</span><span class="p">,</span><span class="n" style="color: #333;">xmm8</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (3) */</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="c"></span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute right */</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="p">);</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="c"></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_pd</span><span class="p">(</span><span class="n" style="color: #333;">rmat</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">xmm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm4</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="c"> </span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate (b13*d1 + b14*d2 | b15*d3 + b16*d4) */</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="c"> <span class="n" style="color: #333;">xmm7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm8</span><span class="p">,</span><span class="n" style="color: #333;">xmm9</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* needed (4) */</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="c"> </span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">xmm8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span><span class="n" style="color: #333;">xmm6</span><span class="p">);</span></span>
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531
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_hadd_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm5</span><span class="p">,</span><span class="n" style="color: #333;">xmm7</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="c"> <span class="n" style="color: #333;">xmm9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">xmm8</span><span class="p">,</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_pd</span><span class="p">(</span><span class="n" style="color: #333;">clv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">xmm9</span><span class="p">);</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="c"></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">clv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="c"> <span class="n" style="color: #333;">lclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="c"> <span class="n" style="color: #333;">rclv</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="c"> <span class="p">}</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="c"><span class="p">}</span></span>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ConditonalPNode</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inode</span><span class="p">)</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="c"><span class="p">{</span></span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">npatt</span><span class="p">;</span></span>
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545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="n" style="color: #333;">lchild</span><span class="p">,</span> <span class="n" style="color: #333;">rchild</span><span class="p">;</span></span>
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547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* recursive call the ConditionalPNode on all children of the current node */</span></span>
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549
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">nson</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="c"> <span class="p">{</span></span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get id of i-th child of current node */</span></span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="c"> <span class="n" style="color: #333;">child</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* if child is an inner node then recursively compute its conditional</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> probabilities vector */</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">child</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mcmc</span><span class="p">.</span><span class="n" style="color: #333;">saveconP</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">oldconP</span><span class="p">[</span><span class="n" style="color: #333;">child</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="c"> <span class="n" style="color: #333;">ConditonalPNode</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="c"> <span class="p">}</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize CLV entries of current node to 1 */</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">states</span><span class="p">;</span></span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="c"> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="c"></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="c"> <span class="n" style="color: #333;">lchild</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="c"> <span class="n" style="color: #333;">rchild</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ltip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">lchild</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rtip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">rchild</span><span class="p">].</span><span class="n" style="color: #333;">nson</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="c"></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ltip</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rtip</span><span class="p">)</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="c"> <span class="p">{</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="c"> <span class="n" style="color: #333;">tip_tip</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="c"> <span class="p">{</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//assert(0);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="c"> <span class="n" style="color: #333;">tip_tip_amb</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="c"> <span class="p">}</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="c"> <span class="p">}</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ltip</span><span class="p">)</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="c"> <span class="p">{</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">)</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="c"> <span class="p">{</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner_amb</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//assert(0);</span></span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="c"> <span class="p">}</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="c"> <span class="p">}</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rtip</span><span class="p">)</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="c"> <span class="p">{</span></span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">cleandata</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner</span><span class="p">(</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//assert(0);</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">tip_inner_amb</span><span class="p">(</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="c"> <span class="n" style="color: #333;">inner_inner</span><span class="p">(</span><span class="n" style="color: #333;">lchild</span><span class="p">,</span><span class="n" style="color: #333;">rchild</span><span class="p">,</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">conP</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="c"><span class="p">}</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1756,7 +1756,8 @@ double rndLaplace(void) {</td>
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1757" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">rndt2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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1758
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1758
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<pre style="margin: 0;"> <span id="LC1758" class="line" lang="c"><span class="p">{</span></span>
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1759
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<pre style="margin: 0;">-<span id="LC1759" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Standard Student's t_2 variate, with d.f. = 2. t2 has mean 0 and variance infinity. */</span></span>
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Standard Student's t_2 variate, with d.f. = 2. t2 has mean 0 and variance infinity. </span></span>
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1761
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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">t2</span><span class="p">;</span></span>
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1761
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1762
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<pre style="margin: 0;"> <span id="LC1762" class="line" lang="c"></span>
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1763
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<pre style="margin: 0;"> <span id="LC1763" class="line" lang="c"> <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rndu</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1772,9 +1773,9 @@ double rndt4(void)</td>
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1772
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<pre style="margin: 0;"> <span id="LC1773" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This has variance 1, and is the standard t4 variate divided by sqrt(2).</span></span>
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<pre style="margin: 0;"> <span id="LC1774" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> The standard t4 variate has variance 2.</span></span>
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<pre style="margin: 0;"> <span id="LC1775" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC1775" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="n" style="color: #333;">c2</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">t4</span><span class="p">,</span> <span class="n" style="color: #333;">sqrt2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">707106781</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="n" style="color: #333;">c2</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">t4</span><span class="p">,</span> <span class="n" style="color: #333;">sqrt2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">707106781<span class="idiff left right">1865475244</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1777" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC1777" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="idiff left right"> </span><span class="p">;</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1779" class="line" lang="c"> <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rndu</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1780
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="c"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rndu</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="c"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4525,7 +4526,7 @@ double Binomial(double n, int k, double *scale)</td>
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<pre style="margin: 0;"> <span id="LC4526" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculates (n choose k), where n is any real number, and k is integer.</span></span>
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<pre style="margin: 0;"> <span id="LC4527" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> If(*scale!=0) the result should be c+exp(*scale).</span></span>
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4528
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<pre style="margin: 0;"> <span id="LC4528" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC4528" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">large</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e<span class="idiff left right">99</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4529" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">large</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e<span class="idiff left right">200</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4530" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4531" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4532" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5676,12 +5677,12 @@ int DescriptiveStatistics(FILE *fout, char infile[], int nbin, int propternary,</td>
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5676
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5677
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<pre style="margin: 0;"> <span id="LC5677" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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5677
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5678
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<pre style="margin: 0;"> <span id="LC5678" class="line" lang="c"> <span class="n" style="color: #333;">fscanf</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">,</span> <span class="s" style="color: #d14;">"%lf"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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5678
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5679
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<pre style="margin: 0;"> <span id="LC5679" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">);</span></span>
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5679
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<pre style="margin: 0;">-<span id="LC5679" class="line" lang="c"></span>
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5680
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<pre style="margin: 0;">+<span id="LC5680" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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5680
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5681
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<pre style="margin: 0;"> <span id="LC5681" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(p>1) {</span></span>
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5681
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5682
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<pre style="margin: 0;"> <span id="LC5682" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> printf("\nGreat offer! I can smooth a few 2-D densities for free. How many do you want? ");</span></span>
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5682
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5683
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<pre style="margin: 0;"> <span id="LC5683" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> scanf("%d", &nf2d);</span></span>
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5683
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5684
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<pre style="margin: 0;"> <span id="LC5684" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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5684
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<pre style="margin: 0;">-<span id="LC5684" class="line" lang="c"> </span>
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5685
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<pre style="margin: 0;">+<span id="LC5685" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">*/</span></span> </span>
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5685
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5686
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<pre style="margin: 0;"> <span id="LC5686" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nf2d</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">MAXNF2D</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"I don't want to do that many!"</span><span class="p">);</span></span>
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5686
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5687
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<pre style="margin: 0;"> <span id="LC5687" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nf2d</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5687
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5688
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<pre style="margin: 0;"> <span id="LC5688" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"pair #%d (e.g., type 1 3 to use variables #1 and #3)? "</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5735,6 +5736,8 @@ int DescriptiveStatistics(FILE *fout, char infile[], int nbin, int propternary,</td>
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5735
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5736
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<pre style="margin: 0;"> <span id="LC5736" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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5736
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5737
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<pre style="margin: 0;"> <span id="LC5737" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">);</span></span>
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5737
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5738
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<pre style="margin: 0;"> <span id="LC5738" class="line" lang="c"></span>
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5739
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<pre style="margin: 0;">+<span id="LC5739" class="line" lang="c"><span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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5740
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<pre style="margin: 0;">+<span id="LC5740" class="line" lang="c"></span>
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5738
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5741
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<pre style="margin: 0;"> <span id="LC5741" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Correlation matrix"</span><span class="p">);</span></span>
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5739
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5742
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<pre style="margin: 0;"> <span id="LC5742" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SkipColumns</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5743
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<pre style="margin: 0;"> <span id="LC5743" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%-8s "</span><span class="p">,</span> <span class="n" style="color: #333;">varstr</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<a href="https://salsa.debian.org/med-team/paml/commit/cdd16ab790640866f7c86c763d62de228be2bf99#a38117fbc1bdd77b43c1c50e6dda570e0ba75c72"><strong>src/treesub.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -936,7 +936,7 @@ int ReadSeq(FILE *fout, FILE *fseq, int cleandata, int locus)</td>
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="c"></span>
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937
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="c"></span>
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/***** GIBBON, 2017.10.8 **/</span></span>
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939
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/<span class="idiff left right">/return(0);</span></span></span>
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/<span class="idiff left right">* return(0); */</span></span></span>
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">readpattern</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="c"> <span class="n" style="color: #333;">PatternWeight</span><span class="p">();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2907,9 +2907,9 @@ int GetTreeFileType(FILE *ftree, int *ntree, int *pauptree, int shortform)</td>
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2907
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<pre style="margin: 0;"> <span id="LC2907" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">PopPaupTree</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ftree</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2908" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">PopPaupTree</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ftree</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2909" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2910" class="line" lang="c"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/* This reads out the string in front of the tree in the nexus format,</span></span>
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<pre style="margin: 0;">-<span id="LC2911" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>typically "tree PAUP_1 = [&U]" with "[&U]" optional</span></span>
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<pre style="margin: 0;">-<span id="LC2912" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span>*/</span></span>
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<pre style="margin: 0;">+<span id="LC2910" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* This reads out the string in front of the tree in the nexus format,</span></span>
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<pre style="margin: 0;">+<span id="LC2911" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> typically "tree PAUP_1 = [&U]" with "[&U]" optional</span></span>
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<pre style="margin: 0;">+<span id="LC2912" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC2913" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ch</span><span class="p">;</span></span>
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2914
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2914
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<pre style="margin: 0;"> <span id="LC2914" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="p">;)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2927,12 +2927,12 @@ int PopPaupTree(FILE *ftree)</td>
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<pre style="margin: 0;"> <span id="LC2927" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2928" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">DownTreeCladeLabel</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">label</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2929" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2930" class="line" lang="c"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/* This goes down the tree to change $ labels (stored in nodes[].label2) into</span></span>
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<pre style="margin: 0;">-<span id="LC2931" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span># labels (stored in nodes[].label). To deal with nested clade labels,</span></span>
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<pre style="margin: 0;">-<span id="LC2932" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>branches within a clade are labeled by negative numbers initially, and</span></span>
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<pre style="margin: 0;">-<span id="LC2933" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>converted to positive labels at the end of the algorithm.</span></span>
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<pre style="margin: 0;">-<span id="LC2934" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>nodes[].label and nodes[].label2 are initialized to -1 before this routine is called.</span></span>
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<pre style="margin: 0;">-<span id="LC2935" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span>*/</span></span>
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<pre style="margin: 0;">+<span id="LC2930" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* This goes down the tree to change $ labels (stored in nodes[].label2) into</span></span>
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<pre style="margin: 0;">+<span id="LC2931" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> # labels (stored in nodes[].label). To deal with nested clade labels,</span></span>
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<pre style="margin: 0;">+<span id="LC2932" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> branches within a clade are labeled by negative numbers initially, and</span></span>
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<pre style="margin: 0;">+<span id="LC2933" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> converted to positive labels at the end of the algorithm.</span></span>
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<pre style="margin: 0;">+<span id="LC2934" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> nodes[].label and nodes[].label2 are initialized to -1 before this routine is called.</span></span>
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<pre style="margin: 0;">+<span id="LC2935" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC2936" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2937" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2938" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3130,7 +3130,7 @@ int ReadTreeN(FILE *ftree, int *haslength, int copyname, int popline)</td>
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<pre style="margin: 0;"> <span id="LC3130" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* label or annotation (node can be tip or internal node) */</span></span>
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<pre style="margin: 0;"> <span id="LC3131" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">quote</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ch</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3132" class="line" lang="c"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReadUntil</span><span class="p">(</span><span class="n" style="color: #333;">ftree</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">quote</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">lline</span><span class="p">);</span></span>
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3133
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<pre style="margin: 0;">-<span id="LC3133" class="line" lang="c"> <span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fgetc</span><span class="p">(</span><span class="n" style="color: #333;">ftree</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* pop off '" */</span></span>
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3133
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<pre style="margin: 0;">+<span id="LC3133" class="line" lang="c"> <span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fgetc</span><span class="p">(</span><span class="n" style="color: #333;">ftree</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* pop off '<span class="idiff left right"> </span>" */</span></span>
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3134
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3134
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<pre style="margin: 0;"> <span id="LC3134" class="line" lang="c"> <span class="p">}</span></span>
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3135
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3135
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<pre style="margin: 0;"> <span id="LC3135" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3136
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3136
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<pre style="margin: 0;"> <span id="LC3136" class="line" lang="c"> <span class="n" style="color: #333;">ungetc</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">,</span> <span class="n" style="color: #333;">ftree</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3140,8 +3140,10 @@ int ReadTreeN(FILE *ftree, int *haslength, int copyname, int popline)</td>
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3140
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3140
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<pre style="margin: 0;"> <span id="LC3140" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">annotation</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"oom annotation"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="3141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3141
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3141
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<pre style="margin: 0;"> <span id="LC3141" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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3142
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3142
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<pre style="margin: 0;"> <span id="LC3142" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* This line is used in MCcoal. ProcessNodeAnnotation is used to process node annotation elsewhere. */</span></span>
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3143
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<pre style="margin: 0;">-<span id="LC3143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3143
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<pre style="margin: 0;">+<span id="LC3143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span><span class="idiff left"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* branch labels used in baseml and codeml */</span></span></span>
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3144
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3144
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<pre style="margin: 0;"> <span id="LC3144" class="line" lang="c"> <span class="n" style="color: #333;">sscanf</span><span class="p">(</span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"%lf"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label</span><span class="p">);</span></span>
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3145
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<pre style="margin: 0;">+<span id="LC3145" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'$'</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* clade labels used to label branches in baseml and codeml */</span></span>
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3146
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<pre style="margin: 0;">+<span id="LC3146" class="line" lang="c"> <span class="n" style="color: #333;">sscanf</span><span class="p">(</span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"%lf"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label2</span><span class="p">);</span></span>
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3145
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3147
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<pre style="margin: 0;"> <span id="LC3147" class="line" lang="c"> <span class="p">}</span></span>
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3146
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3148
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<pre style="margin: 0;"> <span id="LC3148" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* for( ; ; ) */</span></span>
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3147
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3149
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<pre style="margin: 0;"> <span id="LC3149" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3195,9 +3197,15 @@ int OutSubTreeN(FILE *fout, int inode, int spnames, int printopt)</td>
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3195
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3197
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<pre style="margin: 0;"> <span id="LC3197" class="line" lang="c"> <span class="p">}</span></span>
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3196
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3198
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<pre style="margin: 0;"> <span id="LC3198" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">printopt</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">PrNodeNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">nson</span><span class="p">)</span></span>
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3197
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3199
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<pre style="margin: 0;"> <span id="LC3199" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" %d "</span><span class="p">,</span> <span class="n" style="color: #333;">inode</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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3200
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<pre style="margin: 0;">+<span id="LC3200" class="line" lang="c"></span>
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3201
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<pre style="margin: 0;">+<span id="LC3201" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if (defined BPP)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3202
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<pre style="margin: 0;">+<span id="LC3202" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">printopt</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">PrNodeStr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">inode</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">ns</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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3203
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<pre style="margin: 0;">+<span id="LC3203" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" [&theta=%.6f]"</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3204
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<pre style="margin: 0;">+<span id="LC3204" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3198
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<td class="diff-line-num new_line" data-linenumber="3205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3205
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<pre style="margin: 0;"> <span id="LC3205" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">printopt</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">PrLabel</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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3199
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<td class="diff-line-num new_line" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3206
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<pre style="margin: 0;"> <span id="LC3206" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" #%.6f"</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">label</span><span class="p">);</span></span>
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3200
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3207
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<pre style="margin: 0;"> <span id="LC3207" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* fprintf(fout, " [&label=%.6f]", nodes[inode].label); */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3208
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<pre style="margin: 0;">+<span id="LC3208" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3201
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3209
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<pre style="margin: 0;"> <span id="LC3209" class="line" lang="c"></span>
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3202
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3210
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<pre style="margin: 0;"> <span id="LC3210" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">printopt</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">PrAge</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">)</span></span>
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3203
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3211
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<pre style="margin: 0;"> <span id="LC3211" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="s" style="color: #d14;">" @%.6f"</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">inode</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8544,10 +8552,9 @@ int ProcessNodeAnnotation(int *haslabel)</td>
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8544
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8552
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<pre style="margin: 0;"> <span id="LC8552" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fossil</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="8545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8545
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<td class="diff-line-num new_line" data-linenumber="8553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8553
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<pre style="margin: 0;"> <span id="LC8553" class="line" lang="c"> <span class="n" style="color: #333;">pch2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">pch</span><span class="p">,</span> <span class="n" style="color: #333;">braces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="8546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8546
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<td class="diff-line-num new_line" data-linenumber="8554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8554
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<pre style="margin: 0;"> <span id="LC8554" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pch2</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">pch2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">pch</span><span class="p">,</span> <span class="n" style="color: #333;">braces</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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8547
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<td class="diff-line-num new_line old" data-linenumber="8555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8547" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pch2</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8548
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<td class="diff-line-num new_line old" data-linenumber="8555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8548" class="line" lang="c"> <span class="n" style="color: #333;">pch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pch2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8549
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<pre style="margin: 0;">-<span id="LC8549" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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8550
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<pre style="margin: 0;">-<span id="LC8550" class="line" lang="c"> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"did not find left brace"</span><span class="p">);</span></span>
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8555
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<pre style="margin: 0;">+<span id="LC8555" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pch2</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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8556
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<pre style="margin: 0;">+<span id="LC8556" class="line" lang="c"> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"did not find left brace"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8557
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<pre style="margin: 0;">+<span id="LC8557" class="line" lang="c"> <span class="n" style="color: #333;">pch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pch2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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8551
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8558
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<pre style="margin: 0;"> <span id="LC8558" class="line" lang="c"></span>
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8552
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8559
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<pre style="margin: 0;"> <span id="LC8559" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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8553
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<td class="diff-line-num new_line" data-linenumber="8560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8560
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<pre style="margin: 0;"> <span id="LC8560" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="n" style="color: #333;">LOWER_F</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8693,7 +8700,8 @@ int ProcessNodeAnnotation(int *haslabel)</td>
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8693
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8700
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<pre style="margin: 0;"> <span id="LC8700" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">nbtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">nnode</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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8694
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<td class="diff-line-num new_line" data-linenumber="8701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8701
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<pre style="margin: 0;"> <span id="LC8701" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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8695
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<td class="diff-line-num new_line" data-linenumber="8702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8702
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<pre style="margin: 0;"> <span id="LC8702" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">label</span><span class="p">;</span></span>
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8696
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<td class="diff-line-num new_line old" data-linenumber="8703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8696" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">nbtype</span><span class="p">)</span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">nbtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8703
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<pre style="margin: 0;">+<span id="LC8703" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">nbtype</span><span class="p">)</span> </span>
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8704
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<pre style="margin: 0;">+<span id="LC8704" class="line" lang="c"> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">nbtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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8697
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8705
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<pre style="margin: 0;"> <span id="LC8705" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">nbranch</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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8698
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<td class="diff-line-num new_line" data-linenumber="8706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8706
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<pre style="margin: 0;"> <span id="LC8706" class="line" lang="c"> <span class="n" style="color: #333;">error2</span><span class="p">(</span><span class="s" style="color: #d14;">"branch label in the tree (note labels start from 0 and are consecutive)"</span><span class="p">);</span></span>
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8699
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8707
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<pre style="margin: 0;"> <span id="LC8707" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8953,13 +8961,17 @@ void copySptree(void)</td>
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8953
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8961
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<pre style="margin: 0;"> <span id="LC8961" class="line" lang="c"></span>
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8954
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8962
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<pre style="margin: 0;"> <span id="LC8962" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printStree</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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8955
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8963
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<pre style="margin: 0;"> <span id="LC8963" class="line" lang="c"><span class="p">{</span></span>
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8956
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<pre style="margin: 0;">-<span id="LC8956" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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8964
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<pre style="margin: 0;">+<span id="LC8964" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">maxlname</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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8965
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<pre style="margin: 0;">+<span id="LC8965" class="line" lang="c"></span>
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8966
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<pre style="margin: 0;">+<span id="LC8966" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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8967
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<pre style="margin: 0;">+<span id="LC8967" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxlname</span><span class="p">)</span> </span>
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8968
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<pre style="margin: 0;">+<span id="LC8968" class="line" lang="c"> <span class="n" style="color: #333;">maxlname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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8957
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8969
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<pre style="margin: 0;"> <span id="LC8969" class="line" lang="c"></span>
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8958
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8970
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<pre style="margin: 0;"> <span id="LC8970" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">************</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Species tree</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ns = %d nnode = %d"</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nspecies</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nnode</span><span class="p">);</span></span>
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8959
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<td class="diff-line-num new_line old" data-linenumber="8971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8959" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%7s%7s %-<span class="idiff left">16s %8s %8s%16s</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"father"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"node"</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"time"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sons"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fossil"</span><span class="p">);</span></span>
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8971
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<pre style="margin: 0;">+<span id="LC8971" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%7s%7s %-<span class="idiff left">*s %9s %8s%16s</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"father"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"node"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxlname</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"time"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sons"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fossil"</span><span class="p">);</span></span>
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8960
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8972
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<pre style="margin: 0;"> <span id="LC8972" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nnode</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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8961
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<td class="diff-line-num new_line old" data-linenumber="8973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8961" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%7d%7d %-<span class="idiff left right">20s %7</span>.5f"</span><span class="p">,</span></span>
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8962
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<td class="diff-line-num new_line old" data-linenumber="8973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8962" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">father</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">);</span></span>
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8973
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<pre style="margin: 0;">+<span id="LC8973" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%7d%7d %-<span class="idiff left right">*s %8</span>.5f"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8974
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<pre style="margin: 0;">+<span id="LC8974" class="line" lang="c"> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">father</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">maxlname</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">age</span><span class="p">);</span></span>
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8975
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<pre style="margin: 0;"> <span id="LC8975" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">nson</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="8964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8964
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<td class="diff-line-num new_line" data-linenumber="8976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8976
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<pre style="margin: 0;"> <span id="LC8976" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" (%2d %2d)"</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stree</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sons</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="8965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8965
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<td class="diff-line-num new_line" data-linenumber="8977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8977
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<pre style="margin: 0;"> <span id="LC8977" class="line" lang="c"></span>
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