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GitLab

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<h3>

Steffen Möller pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/python-treetime">Debian Med / python-treetime</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39">b3255387</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-03T20:08:48+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.7.5</pre>

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</ul>

<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#4c23f3e77a0ef00cf8da63e8e50eef5197724f75">

changelog.md

</a>

</li>

<li class="file-stats">

<a href="#716e6f6c16580800d13452615e2c01668aacc288">

treetime/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#9197866d72ee7afc1de2097e1da379c23f68c559">

treetime/distribution.py

</a>

</li>

<li class="file-stats">

<a href="#b990c4f689cacd4a1e8800b187c4078a5c5ed01f">

treetime/gtr.py

</a>

</li>

<li class="file-stats">

<a href="#ea6325c04095908d06ab422a724a6b1ff8dbdd51">

treetime/merger_models.py

</a>

</li>

<li class="file-stats">

<a href="#5233e2843fb208ffac5520b8b6d010090372931b">

treetime/sequence_data.py

</a>

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<li class="file-stats">

<a href="#6624cff14dcfe6502cafe07be4ddc0373a1b7838">

<span class="deleted-file">

−

treetime/test_opt.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#a2e471fd9fc09543e8fd92727442680e1b76576b">

treetime/treeanc.py

</a>

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<li class="file-stats">

<a href="#0994bbb65b28bed19201420b96136d5e9f676859">

treetime/treetime.py

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<li class="file-stats">

<a href="#b73718dcdf4bacd94dd536b6bb62ded9789d6bc5">

treetime/utils.py

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<li class="file-stats">

<a href="#884b9238819e29c9c3a7ccd69fd2f6ed9f2fab18">

treetime/wrappers.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="4c23f3e77a0ef00cf8da63e8e50eef5197724f75">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#4c23f3e77a0ef00cf8da63e8e50eef5197724f75"><strong>changelog.md</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.7.5 -- fix desync of peak from grid of distributions after pruning </span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.7.4 -- bug fix in reconstruct discrete trait routine</span></span>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`reconstruct_discrete_traits`</span> wrapper function didn't handle missing data correctly (after the changed released in 0.7.2) which resulted in alphabets and weights of different lengths.</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.7.3 -- bug fix in average rate calculation</span></span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">This release fixes a problem that surfaced when inferring GTR models from trees of very similar sequences but quite a few gaps. This resulted in mutation counts like so:</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">A: [[ 0.  1.  8.  3.  0.]</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">C:  [ 1.  0.  2.  7.  0.]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">G:  [ 9.  0.  0.  2.  0.]</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">T:  [ 1. 23.  6.  0.  0.]</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">-:  [46. 22. 28. 38.  0.]]</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">As a result, the rate "to gap" is inferred quite high, while the equilibrium gap fraction is low. Since we cap the equilibrium gap fraction from below to avoid reconstruction problems when branches are very short, this resulted in an average rate that had substantial contribution from and assumed 1% equilibrum gap frequency where gaps mutate at 20times the rate as others. Since gaps are ignored in distance calculations anyway, it is more sensible to exclude these transitions from the calculation of the average rate. This is now happening in line 7 of treetime/gtr.py. The average rate is restricted to mutation substitutions from non-gap states to any state.</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.7.2 -- weights in discrete trait reconstruction</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">This release implements a more consistent handling of weights (fixed equilibrium frequencies) in discrete state reconstruction.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">It also fixes a number of problems in who the arguments were processed.</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">TreeTime now allows</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p"> *</span> unobserved discrete states</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p"> *</span> uses expected time-in-tree instead of observed time-in-tree in GTR estimation when weights are fixed. The former resulted in very unstable rate estimates.</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.7.0 -- restructuring</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Major changes</span></span>

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<br>

</li>

<li id="716e6f6c16580800d13452615e2c01668aacc288">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#716e6f6c16580800d13452615e2c01668aacc288"><strong>treetime/__init__.py</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.7.<span class="idiff left right">0</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.7.<span class="idiff left right">5</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TreeTimeError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python">    <span class="s" style="color: #d14;">"""TreeTimeError class"""</span></span>

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<li id="9197866d72ee7afc1de2097e1da379c23f68c559">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#9197866d72ee7afc1de2097e1da379c23f68c559"><strong>treetime/distribution.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" 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="265" 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">@@ -265,6 +265,10 @@ class Distribution(object):</td>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">                <span class="n" style="color: #333;">updated</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">                <span class="n" style="color: #333;">n_iter</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="268" 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="268" 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="LC268" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_peak_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_func</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">).</span><span class="n" style="color: #333;">argmin</span><span class="p">()</span></span>

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<td class="diff-line-num new old_line" data-linenumber="268" 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="269" 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="LC269" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_peak_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_func</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_peak_idx</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="268" 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="270" 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="LC270" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_peak_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">peak_pos</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="268" 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="271" 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="LC271" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="269" 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">

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<td class="diff-line-num new_line" data-linenumber="273" 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">

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">prob</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="274" 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">

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</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;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__call__</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">))</span></span>

</pre>

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<li id="b990c4f689cacd4a1e8800b187c4078a5c5ed01f">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#b990c4f689cacd4a1e8800b187c4078a5c5ed01f"><strong>treetime/gtr.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,6 +4,12 @@ import numpy as np</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ttconf</span></span>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

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<td class="diff-line-num new_line" data-linenumber="5" 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.seq_utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">alphabets</span><span class="p">,</span> <span class="n" style="color: #333;">profile_maps</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet_synonyms</span></span>

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<td class="diff-line-num new_line" data-linenumber="6" 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">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">avg_transition</span><span class="p">(</span><span class="n" style="color: #333;">W</span><span class="p">,</span><span class="n" style="color: #333;">pi</span><span class="p">,</span> <span class="n" style="color: #333;">gap_index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gap_index</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">einsum</span><span class="p">(</span><span class="s" style="color: #d14;">'i,ij,j'</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">,</span> <span class="n" style="color: #333;">W</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" 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="LC10" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" 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="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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">einsum</span><span class="p">(</span><span class="s" style="color: #d14;">'i,ij,j'</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">,</span> <span class="n" style="color: #333;">W</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">W</span><span class="p">[:,</span><span class="n" style="color: #333;">gap_index</span><span class="p">])</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pi</span><span class="p">[</span><span class="n" style="color: #333;">gap_index</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pi</span><span class="p">[</span><span class="n" style="color: #333;">gap_index</span><span class="p">])</span></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="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="13" 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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

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<td class="diff-line-num new_line" data-linenumber="14" 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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GTR</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="15" 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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" 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>

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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">@@ -212,7 +218,7 @@ class GTR(object):</td>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_W</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">W</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">W</span><span class="p">.</span><span class="n" style="color: #333;">T</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python">        <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">fill_diagonal</span><span class="p">(</span><span class="n" style="color: #333;">W</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">        <span class="n" style="color: #333;">average_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">W</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">dot</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Pi</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">dot</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">Pi</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python">        <span class="n" style="color: #333;">average_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">avg_transition</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">W</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Pi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gap_index</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">gap_index</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_W</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">average_rate</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mu</span> <span class="o" style="font-weight: 600;">*=</span><span class="n" style="color: #333;">average_rate</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"></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">@@ -378,23 +384,27 @@ class GTR(object):</td>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.aa_models</span>  <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">JTT92</span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="380" 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">

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<td class="diff-line-num new_line" data-linenumber="386" 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">

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'jc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jc69'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jukes-cantor'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jukes-cantor69'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jukescantor'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jukescantor69'</span><span class="p">]:</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">JC69</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="382" 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="387" 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="LC387" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">JC69</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="382" 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">

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<td class="diff-line-num new_line" data-linenumber="388" 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">

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'k80'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kimura80'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kimura1980'</span><span class="p">]:</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">K80</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="389" 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="LC389" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">K80</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="390" 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">

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'f81'</span><span class="p">,</span> <span class="s" style="color: #d14;">'felsenstein81'</span><span class="p">,</span> <span class="s" style="color: #d14;">'felsenstein1981'</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">F81</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="386" 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="391" 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="LC391" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">F81</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="392" 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">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'hky'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hky85'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hky1985'</span><span class="p">]:</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">HKY85</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="393" 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="LC393" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">HKY85</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="394" 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">

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'t92'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tamura92'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tamura1992'</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">T92</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="390" 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="395" 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="LC395" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">T92</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="396" 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">

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'tn93'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tamura_nei_93'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tamuranei93'</span><span class="p">]:</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">

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<td class="diff-line-num new_line old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">TN93</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="392" 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="397" 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="LC397" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">TN93</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="398" 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">

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'jtt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jtt92'</span><span class="p">]:</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">

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<td class="diff-line-num new_line old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">            <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">JTT92</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="394" 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="399" 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="LC399" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">model</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">JTT92</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="394" 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">

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<td class="diff-line-num new_line" data-linenumber="400" 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">

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="395" 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">

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<td class="diff-line-num new_line" data-linenumber="401" 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">

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">"The GTR model '{}' is not in the list of available models."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="396" 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">

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<td class="diff-line-num new_line" data-linenumber="402" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC402" class="line" lang="python">                <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="397" 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">

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<td class="diff-line-num new_line" data-linenumber="403" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" 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="404" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC404" class="line" lang="python">        <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">mu</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'mu'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'mu'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">1.0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="405" 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">

405

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC405" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="406" 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">

406

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" 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="407" 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">

407

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="398" 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">

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<td class="diff-line-num new_line" data-linenumber="408" 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">

408

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC408" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" 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">

399

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<td class="diff-line-num new_line" data-linenumber="409" 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">

409

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">random</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">mu</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nuc'</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python">        <span class="s" style="color: #d14;">"""</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">@@ -494,13 +504,16 @@ class GTR(object):</td>

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python">                                                    <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</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;">pc_mat</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python">            <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">fill_diagonal</span><span class="p">(</span><span class="n" style="color: #333;">W_ij</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="LC497" class="line" lang="python">            <span class="n" style="color: #333;">scale_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">einsum</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'i,ij,j'</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">pi</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">W_ij</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">pi</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python">            <span class="n" style="color: #333;">scale_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">avg_transition</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">W_ij</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">pi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gap_index</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">gtr</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">gap_index</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python">            <span class="n" style="color: #333;">W_ij</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W_ij</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">scale_factor</span></span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fixed_pi</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python">                <span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">nij</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pc_mat</span><span class="p">,</span><span class="n" style="color: #333;">axis</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="n" style="color: #333;">root_state</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mu</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="n" style="color: #333;">W_ij</span><span class="p">,</span><span class="n" style="color: #333;">Ti</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">root_state</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">pc_mat</span><span class="p">,</span> <span class="n" style="color: #333;">axis</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="LC512" class="line" lang="python">                <span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>

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<td class="diff-line-num new_line old" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python">            <span class="n" style="color: #333;">mu</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nij</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">W_ij</span><span class="p">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="n" style="color: #333;">Ti</span><span class="p">))))</span></span>

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python">                <span class="n" style="color: #333;">mu</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nij</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">W_ij</span><span class="p">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="n" style="color: #333;">Ti</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="514" 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">

514

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="504" 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="515" 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">

515

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python">                <span class="n" style="color: #333;">mu</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nij</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">W_ij</span><span class="p">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">)))</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Ti</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="504" 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="516" 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">

516

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="504" 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">

504

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<td class="diff-line-num new_line" data-linenumber="517" 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">

517

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">Nit</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="505" 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">

505

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<td class="diff-line-num new_line" data-linenumber="518" 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">

518

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python">            <span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="s" style="color: #d14;">'WARNING: maximum number of iterations has been reached in GTR inference'</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">warn</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="519" 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">

519

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">LA</span><span class="p">.</span><span class="n" style="color: #333;">norm</span><span class="p">(</span><span class="n" style="color: #333;">pi_old</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dp</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="999" 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="1012" 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">@@ -999,7 +1012,7 @@ class GTR(object):</td>

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1012

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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="python">                      <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">si</span><span class="p">,</span><span class="n" style="color: #333;">state</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">)])</span></span>

</pre>

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1000

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<td class="diff-line-num new_line" data-linenumber="1013" 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">

1013

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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1001" 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">

1001

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<td class="diff-line-num new_line" data-linenumber="1014" 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">

1014

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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">average_rate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1002

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<td class="diff-line-num new_line old" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mu</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">einsum</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'ii,i'</span></span><span class="p"><span class="idiff">,</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Q</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">Pi</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1003" 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="1015" 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">

1015

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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mu</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">avg_transition</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">W</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Pi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gap_index</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">gap_index</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1003" 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">

1003

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<td class="diff-line-num new_line" data-linenumber="1016" 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">

1016

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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1004" 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">

1004

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<td class="diff-line-num new_line" data-linenumber="1017" 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">

1017

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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">save_to_npz</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1005" 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">

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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="python">        <span class="n" style="color: #333;">full_gtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mu</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">Pi</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">W</span><span class="p">)</span></span>

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<li id="ea6325c04095908d06ab422a724a6b1ff8dbdd51">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#ea6325c04095908d06ab422a724a6b1ff8dbdd51"><strong>treetime/merger_models.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" 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">@@ -33,12 +33,14 @@ class Coalescent(object):</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">            - Tc:   a float or an iterable, if iterable another argument T of same shape is required</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">            - T:    an array like of same shape as Tc that specifies the time pivots corresponding to Tc</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">                    note that this array is ordered past to present corresponding to</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">                    decreasing 'time before present' values</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">            - None</span></span>

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<td class="diff-line-num new_line" data-linenumber="40" 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">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;">        '''</span></span>

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<td class="diff-line-num new_line" data-linenumber="41" 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">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">Tc</span><span class="p">,</span> <span class="n" style="color: #333;">Iterable</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="42" 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">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">Tc</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">len</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 new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python">                <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">concatenate</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">ttconf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">BIG_NUMBER</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">T</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[</span></span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">BIG_NUMBER</span><span class="p">]))</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">                <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">concatenate</span><span class="p">(([</span><span class="n" style="color: #333;"><span class="idiff left">ttconf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">BIG_NUMBER</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">T</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-</span></span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">BIG_NUMBER</span><span class="p">]))</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">                <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">concatenate</span><span class="p">(([</span><span class="n" style="color: #333;">Tc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span> <span class="n" style="color: #333;">Tc</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">Tc</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="LC45" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">Tc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interp1d</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<li id="5233e2843fb208ffac5520b8b6d010090372931b">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#5233e2843fb208ffac5520b8b6d010090372931b"><strong>treetime/sequence_data.py</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">@@ -161,11 +161,11 @@ class SequenceData(object):</td>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">in_aln</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># check whether the alignment is consistent with a nucleotide alignment.</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_alphabet</span><span class="p">([</span><span class="n" style="color: #333;">seq2array</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_aln</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_sparse</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">seq2array</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">convert_upper</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">convert_upper</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">                                           <span class="n" style="color: #333;">fill_overhangs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fill_overhangs</span><span class="p">,</span> <span class="n" style="color: #333;">ambiguous</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">                         <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_aln</span><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_alphabet</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_aln</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()))</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_sparse</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="s" style="color: #d14;">"SequenceData: loaded alignment."</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="LC170" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">in_aln</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">,</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="s" style="color: #d14;">"SequenceData: loaded sparse/vcf alignment."</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<li id="6624cff14dcfe6502cafe07be4ddc0373a1b7838">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#6624cff14dcfe6502cafe07be4ddc0373a1b7838"><strong>treetime/test_opt.py</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">optimize_tree_marginal_new</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">damping</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python">        <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">compressed_length</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python">        <span class="n" style="color: #333;">n_states</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">shape</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="LC4" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># propagate leaves --> root, set the marginal-likelihood messages</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">find_clades</span><span class="p">(</span><span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'postorder'</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;">#leaves -> root</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">up</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">clades</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>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python">            <span class="n" style="color: #333;">profiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python">            <span class="n" style="color: #333;">bls</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nodes</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python">            <span class="n" style="color: #333;">new_bls</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_star</span><span class="p">(</span><span class="n" style="color: #333;">profiles</span><span class="p">,</span><span class="n" style="color: #333;">bls</span><span class="p">,</span> <span class="n" style="color: #333;">last_is_root</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">up</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># regardless of what was before, set the profile to ones</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python">            <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">((</span><span class="n" style="color: #333;">L</span><span class="p">,</span><span class="n" style="color: #333;">n_states</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python">            <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ch</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ci</span><span class="p">,</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python">                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_bls</span><span class="p">[</span><span class="n" style="color: #333;">ci</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python">                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">propagate_profile</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">                                                                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python">                <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python">            <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_log_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">            <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">offset</span> <span class="c1" style="color: #998; font-style: italic;"># and store log-prefactor</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">up</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">propagate_profile</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">                                                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># raw prob to transfer prob up</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python">                <span class="n" style="color: #333;">tmp_msg_from_parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">evolve</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">,</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python">                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_branch_length_to_gtr</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">),</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_profile</span><span class="p">,</span> <span class="n" style="color: #333;">pre</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp_msg_from_parent</span><span class="p">,</span> <span class="n" style="color: #333;">return_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_profile</span><span class="p">,</span> <span class="n" style="color: #333;">pre</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">,</span> <span class="n" style="color: #333;">return_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python">        <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">root</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">            <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">((</span><span class="n" style="color: #333;">L</span><span class="p">,</span><span class="n" style="color: #333;">n_states</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python">            <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python">            <span class="n" style="color: #333;">old_bl</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;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">branch_length</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;">clades</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 old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python">            <span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">optimal_t_compressed</span><span class="p">((</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">marginal_subtree_LH</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;">marginal_outgroup_LH</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python">                                                <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">),</span> <span class="n" style="color: #333;">multiplicity</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">multiplicity</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python">                                                <span class="n" style="color: #333;">profiles</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">tol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-8</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ch</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">root</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python">                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</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;">damping</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">old_bl</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">damping</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bl</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">old_bl</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python">                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">propagate_profile</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python">                                            <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># raw prob to transfer prob up</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python">                <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python">                <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python">            <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_log_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python">            <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">offset</span> <span class="c1" style="color: #998; font-style: italic;"># and store log-prefactor</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_LH_and_root_sequence</span><span class="p">(</span><span class="n" style="color: #333;">assign_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">preorder_traversal_marginal</span><span class="p">(</span><span class="n" style="color: #333;">assign_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">reconstruct_leaves</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">optimize_tree_marginal_new2</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">n_iter_internal</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;">damping</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python">        <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">compressed_length</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python">        <span class="n" style="color: #333;">n_states</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># propagate leaves --> root, set the marginal-likelihood messages</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">(</span><span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'postorder'</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;">#leaves -> root</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">up</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">clades</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>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># regardless of what was before, set the profile to ones</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ii</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_iter_internal</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python">                <span class="n" style="color: #333;">damp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">damping</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;">ii</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python">                <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">((</span><span class="n" style="color: #333;">L</span><span class="p">,</span><span class="n" style="color: #333;">n_states</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ch</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python">                    <span class="n" style="color: #333;">outgroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">maximum</span><span class="p">(</span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</span><span class="p">,</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_profile</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python">                    <span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">optimal_t_compressed</span><span class="p">((</span><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">outgroup</span><span class="p">),</span> <span class="n" style="color: #333;">multiplicity</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">multiplicity</span><span class="p">,</span> <span class="n" style="color: #333;">profiles</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">tol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-8</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python">                    <span class="n" style="color: #333;">new_bl</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;">damp</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">damp</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">                    <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">new_bl</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python">                    <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">propagate_profile</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python">                                                <span class="n" style="color: #333;">new_bl</span><span class="p">,</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># raw prob to transfer prob up</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">                    <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python">                    <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_log_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python">                <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">offset</span> <span class="c1" style="color: #998; font-style: italic;"># and store log-prefactor</span></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">up</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python">                    <span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">optimal_t_compressed</span><span class="p">((</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">),</span> <span class="n" style="color: #333;">multiplicity</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">multiplicity</span><span class="p">,</span> <span class="n" style="color: #333;">profiles</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">tol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-8</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python">                    <span class="n" style="color: #333;">new_bl</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;">damp</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">damp</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python">                    <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">new_bl</span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python">                    <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">propagate_profile</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python">                                                    <span class="n" style="color: #333;">new_bl</span><span class="p">,</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># raw prob to transfer prob up</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python">                    <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">,</span> <span class="n" style="color: #333;">pre</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">maximum</span><span class="p">(</span><span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">TINY_NUMBER</span><span class="p">,</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">up</span><span class="p">.</span><span class="n" style="color: #333;">marginal_profile</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python">                                                 <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">return_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">                    <span class="n" style="color: #333;">tmp_msg_from_parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">evolve</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python">                                                     <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_branch_length_to_gtr</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">),</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">                    <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_profile</span><span class="p">,</span> <span class="n" style="color: #333;">pre</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp_msg_from_parent</span><span class="p">,</span> <span class="n" style="color: #333;">return_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python">                    <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_profile</span><span class="p">,</span> <span class="n" style="color: #333;">pre</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">marginal_outgroup_LH</span><span class="p">,</span> <span class="n" style="color: #333;">return_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python">        <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">root</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">))</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</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>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python">            <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">((</span><span class="n" style="color: #333;">L</span><span class="p">,</span><span class="n" style="color: #333;">n_states</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python">            <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python">            <span class="n" style="color: #333;">old_bl</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;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">branch_length</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;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python">            <span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">optimal_t_compressed</span><span class="p">((</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">marginal_subtree_LH</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;">marginal_outgroup_LH</span><span class="p">,</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python">                                                <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">),</span> <span class="n" style="color: #333;">multiplicity</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">multiplicity</span><span class="p">,</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python">                                                <span class="n" style="color: #333;">profiles</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">tol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-8</span><span class="p">)</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ch</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">root</span><span class="p">:</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python">                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">bl</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">old_bl</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python">                <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">propagate_profile</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python">                                            <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span> <span class="n" style="color: #333;">return_log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># raw prob to transfer prob up</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python">                <span class="n" style="color: #333;">tmp_log_subtree_LH</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_log_Lx</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python">                <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">            <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_profile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_log_subtree_LH</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python">            <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">marginal_subtree_LH_prefactor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">offset</span> <span class="c1" style="color: #998; font-style: italic;"># and store log-prefactor</span></span>

</pre>

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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="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_LH_and_root_sequence</span><span class="p">(</span><span class="n" style="color: #333;">assign_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">preorder_traversal_marginal</span><span class="p">(</span><span class="n" style="color: #333;">assign_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">reconstruct_leaves</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span></pre>

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<br>

</li>

<li id="a2e471fd9fc09543e8fd92727442680e1b76576b">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#a2e471fd9fc09543e8fd92727442680e1b76576b"><strong>treetime/treeanc.py</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">@@ -312,6 +312,8 @@ class TreeAnc(object):</td>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'TreeAnc: could not load tree! input was '</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">in_tree</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tree</span><span class="p">.</span><span class="n" style="color: #333;">count_terminals</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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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'TreeAnc: tree in %s as only %d tips. Please check your tree!'</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">in_tree</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tree</span><span class="p">.</span><span class="n" style="color: #333;">count_terminals</span><span class="p">()))</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># remove all existing sequence attributes</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tree</span><span class="p">.</span><span class="n" style="color: #333;">find_clades</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">@@ -376,8 +378,8 @@ class TreeAnc(object):</td>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="s" style="color: #d14;">"***WARNING: TreeAnc._attach_sequences_to_nodes: NO SEQUENCE FOR LEAF: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">warn</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">                <span class="n" style="color: #333;">failed_leaves</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">failed_leaves</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">count_terminals</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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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">MissingDataError</span><span class="p">(</span><span class="s" style="color: #d14;">"TreeAnc._check_alignment_tree_gtr_consistency: At least 30</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;"><span class="idiff left right">\</span></span><span class="s" style="color: #d14;">% terminal nodes cannot be assigned a sequence!</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python">                                           <span class="s" style="color: #d14;">"Are you sure the alignment belongs to the tree?"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">warn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">MissingDataError</span><span class="p">(</span><span class="s" style="color: #d14;">"TreeAnc._check_alignment_tree_gtr_consistency: At least 30</span><span class="si" style="color: #d14;">\</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">% </span><span class="se" style="color: #d14;">t</span><span class="s" style="color: #d14;">erminal nodes cannot be assigned a sequence!</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">                                           <span class="s" style="color: #d14;">"Are you sure the alignment belongs to the tree?"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># could not assign sequence for internal node - is OK</span></span>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1284" 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>

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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">branch_length_mode</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'marginal'</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC1287" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_tree_marginal</span><span class="p">(</span><span class="n" style="color: #333;">max_iter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_iter</span><span class="p">,</span> <span class="n" style="color: #333;">infer_gtr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infer_gtr</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_tree_marginal</span><span class="p">(</span><span class="n" style="color: #333;">max_iter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_iter</span><span class="p">,</span> <span class="n" style="color: #333;">infer_gtr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infer_gtr</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1290" 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="LC1290" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prune_short</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1288" 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="1291" 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="LC1291" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prune_short_branches</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1292" 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">

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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">branch_length_mode</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'input'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1293" 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">

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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="python">            <span class="n" style="color: #333;">N_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reconstruct_anc</span><span class="p">(</span><span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'probabilistic'</span><span class="p">,</span> <span class="n" style="color: #333;">infer_gtr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infer_gtr</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pc</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1294" 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">

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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="python">                                          <span class="n" style="color: #333;">marginal</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">marginal_sequences</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC1291" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">success</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1295" 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="LC1295" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prune_short</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prune_short_branches</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1297" 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="LC1297" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ttconf</span><span class="p">.</span><span class="n" style="color: #333;">SUCCESS</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1298" 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">

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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">branch_length_mode</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">'joint'</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="1299" 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">

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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownMethodError</span><span class="p">(</span><span class="s" style="color: #d14;">"TreeAnc.optimize_tree: `branch_length_mode` should be in ['marginal', 'joint', 'input']"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1300" 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">

1300

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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="python"></span>

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</li>

<li id="0994bbb65b28bed19201420b96136d5e9f676859">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#0994bbb65b28bed19201420b96136d5e9f676859"><strong>treetime/treetime.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="441" 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="441" 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">@@ -441,7 +441,7 @@ class TreeTime(ClockTree):</td>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span><span class="n" style="color: #333;">Phylo</span><span class="p">.</span><span class="n" style="color: #333;">BaseTree</span><span class="p">.</span><span class="n" style="color: #333;">Clade</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python">                <span class="n" style="color: #333;">new_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root</span></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python">                <span class="n" style="color: #333;">new_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">common_ancestor</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">root</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python">                <span class="n" style="color: #333;">new_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">common_ancestor</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">root</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_leaves_lookup</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">                <span class="n" style="color: #333;">new_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_leaves_lookup</span><span class="p">[</span><span class="n" style="color: #333;">root</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'oldest'</span><span class="p">:</span></span>

</pre>

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<li id="b73718dcdf4bacd94dd536b6bb62ded9789d6bc5">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#b73718dcdf4bacd94dd536b6bb62ded9789d6bc5"><strong>treetime/utils.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="238" 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">@@ -238,7 +238,7 @@ def parse_dates(date_file, name_col=None, date_col=None):</td>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># read the metadata file into pandas dataframe.</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python">        <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">date_file</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">full_sep</span><span class="p">,</span> <span class="n" style="color: #333;">engine</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'python'</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'str'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">        <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">date_file</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">full_sep</span><span class="p">,</span> <span class="n" style="color: #333;">engine</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'python'</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'str'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">index_col</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># check the metadata has strain names in the first column</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># look for the column containing sampling dates</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># We assume that the dates might be given either in human-readable format</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" 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="293" 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">@@ -293,7 +293,10 @@ def parse_dates(date_file, name_col=None, date_col=None):</td>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">                <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index_col</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># try parsing as a float first</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python">                    <span class="n" style="color: #333;">dates</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="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">date_str</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">date_str</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python">                        <span class="n" style="color: #333;">dates</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="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">date_str</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="297" 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="299" 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="LC299" class="line" lang="python">                        <span class="n" style="color: #333;">dates</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="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num new_line" data-linenumber="300" 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">

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># try whether the date string can be parsed as [2002.2:2004.3]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" 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="321" 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">@@ -318,7 +321,6 @@ def parse_dates(date_file, name_col=None, date_col=None):</td>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="319" 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">

319

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<td class="diff-line-num new_line" data-linenumber="322" 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">

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dates</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="320" 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">

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<td class="diff-line-num new_line" data-linenumber="323" 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">

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TreeTimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Cannot parse dates correctly! Check date format."</span><span class="p">)</span></span>

</pre>

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321

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<td class="diff-line-num new_line old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">)</span></span>

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322

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<td class="diff-line-num new_line" data-linenumber="324" 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">

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dates</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="325" 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">

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">TreeTimeError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="326" 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">

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">err</span></span>

</pre>

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<br>

</li>

<li id="884b9238819e29c9c3a7ccd69fd2f6ed9f2fab18">

<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/b3255387cc32187d30eabd988f41c8cb52011b39#884b9238819e29c9c3a7ccd69fd2f6ed9f2fab18"><strong>treetime/wrappers.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="13" 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">@@ -13,7 +13,7 @@ from treetime import config as ttconf</td>

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13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">utils</span></span>

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<td class="diff-line-num old_line" data-linenumber="14" 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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.vcf_utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_vcf</span><span class="p">,</span> <span class="n" style="color: #333;">write_vcf</span></span>

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<td class="diff-line-num new_line" data-linenumber="15" 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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.seq_utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">alphabets</span></span>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TreeTimeError</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" 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="16" 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="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TreeTimeError</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">MissingDataError</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

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<td class="diff-line-num new_line" data-linenumber="18" 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">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">assure_tree</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'treetime_tmp'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" 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">

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<td class="diff-line-num new_line" data-linenumber="19" 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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="30" 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">@@ -30,7 +30,8 @@ def assure_tree(params, tmp_dir='treetime_tmp'):</td>

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<td class="diff-line-num new_line" data-linenumber="30" 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">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">        <span class="n" style="color: #333;">tt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeAnc</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">TreeTimeError</span><span class="p">,</span> <span class="n" style="color: #333;">MissingDataError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Tree loading/building failed."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

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<td class="diff-line-num new_line" data-linenumber="37" 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">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="711" 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="712" 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">@@ -711,42 +712,72 @@ def reconstruct_discrete_traits(tree, traits, missing_data='?', pc=1.0, sampling</td>

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"><span class="s" style="color: #d14;">    TreeTimeError</span></span>

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"><span class="s" style="color: #d14;">        raise error if ancestral reconstruction errors out</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC714" class="line" lang="python">    <span class="n" style="color: #333;">unique_states</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">traits</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()))</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC715" class="line" lang="python">    <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unique_states</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC716" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">180</span><span class="p">:</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"mugration: can't have more than 180 states!"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC718" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC719" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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720

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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"mugration: only one or zero states found -- this doesn't make any sense"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC721" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

722

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<td class="diff-line-num new_line old" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC722" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="723" 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">

723

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715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

</pre>

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724

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<td class="diff-line-num new_line" data-linenumber="716" 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">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">### make a single character alphabet that maps to discrete states</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="725" 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">

725

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<td class="diff-line-num new_line" data-linenumber="717" 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">

717

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

</pre>

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726

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<td class="diff-line-num new_line old" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC726" class="line" lang="python">    <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="mi" style="color: #099;">65</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">state</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">unique_states</span><span class="p">)]</span></span>

</pre>

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727

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<pre style="margin: 0;">-<span id="LC727" class="line" lang="python">    <span class="n" style="color: #333;">missing_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="mi" style="color: #099;">65</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nc</span><span class="p">)</span></span>

</pre>

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728

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<td class="diff-line-num new_line old" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC728" class="line" lang="python">    <span class="n" style="color: #333;">letter_to_state</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">a</span><span class="p">:</span><span class="n" style="color: #333;">unique_states</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">)}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="719" 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="LC719" class="line" lang="python">    <span class="n" style="color: #333;">unique_states</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">traits</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>

</pre>

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720

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python">    <span class="n" style="color: #333;">n_observed_states</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unique_states</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="721" 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">

721

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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># load weights from file and convert to dict if supplied as string</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="723" 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="LC723" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="724" 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="LC724" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="725" 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="LC725" class="line" lang="python">            <span class="n" style="color: #333;">tmp_weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">t</span><span class="s" style="color: #d14;">'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weights</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 class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'tsv'</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">','</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC726" class="line" lang="python">                                 <span class="n" style="color: #333;">skipinitialspace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="727" 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">

727

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<pre style="margin: 0;">+<span id="LC727" class="line" lang="python">            <span class="n" style="color: #333;">weight_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ri</span><span class="p">,</span><span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp_weights</span><span class="p">.</span><span class="n" style="color: #333;">iterrows</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="728" 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">

728

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC728" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="729" 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">

729

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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Loading of weights file '%s' failed!"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">weights</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="730" 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">

730

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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="731" 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">

731

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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python">        <span class="n" style="color: #333;">weight_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weights</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="732" 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">

732

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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="733" 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">

733

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC733" class="line" lang="python">        <span class="n" style="color: #333;">weight_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="734" 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">

734

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="735" 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">

735

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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># add weights to unique states for alphabet construction</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="736" 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">

736

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC736" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weight_dict</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="737" 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">

737

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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python">        <span class="n" style="color: #333;">unique_states</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">weight_dict</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="738" 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">

738

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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python">        <span class="n" style="color: #333;">missing_weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unique_states</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">weight_dict</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">missing_data</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="739" 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">

739

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC739" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_weights</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="740" 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">

740

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC740" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing weights for values: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">missing_weights</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="741" 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">

741

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="742" 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">

742

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC742" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_weights</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n_observed_states</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="743" 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">

743

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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"More than half of discrete states missing from the weights file"</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="744" 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">

744

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<pre style="margin: 0;">+<span id="LC744" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Weights read from file are:"</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" 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">

745

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<pre style="margin: 0;">+<span id="LC745" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TreeTimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"More than half of discrete states missing from the weights file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="746" 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">

746

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<pre style="margin: 0;">+<span id="LC746" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="747" 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">

747

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<pre style="margin: 0;">+<span id="LC747" class="line" lang="python">    <span class="n" style="color: #333;">unique_states</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">unique_states</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="748" 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">

748

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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># make a map from states (excluding missing data) to characters in the alphabet</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="749" 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">

749

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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># note that gap character '-' is chr(45) and will never be included here</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="729" 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="750" 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">

750

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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python">    <span class="n" style="color: #333;">reverse_alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">state</span><span class="p">:</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="mi" style="color: #099;">65</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">state</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">unique_states</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">missing_data</span><span class="p">}</span></span>

</pre>

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751

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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python">    <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">reverse_alphabet</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>

</pre>

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752

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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># construct a look up from alphabet character to states</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="753" 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">

753

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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python">    <span class="n" style="color: #333;">letter_to_state</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reverse_alphabet</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="754" 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">

754

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<pre style="margin: 0;">+<span id="LC754" class="line" lang="python"></span>

</pre>

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755

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<pre style="margin: 0;">+<span id="LC755" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># construct the vector with weights to be used as equilibrium frequency</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC756" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weight_dict</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC757" class="line" lang="python">        <span class="n" style="color: #333;">mean_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">weight_dict</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python">        <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">weight_dict</span><span class="p">[</span><span class="n" style="color: #333;">letter_to_state</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">letter_to_state</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">weight_dict</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">mean_weight</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python">                            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alphabet</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="760" 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">

760

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC760" class="line" lang="python">        <span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">/=</span><span class="n" style="color: #333;">weights</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="761" 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">

761

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC761" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="762" 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">

762

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC762" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># consistency checks</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="763" 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">

763

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC763" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="764" 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">

764

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC764" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"mugration: only one or zero states found -- this doesn't make any sense"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="765" 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">

765

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC765" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="766" 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">

766

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC766" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="767" 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">

767

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC767" class="line" lang="python">    <span class="n" style="color: #333;">n_states</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="768" 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">

768

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC768" class="line" lang="python">    <span class="n" style="color: #333;">missing_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="mi" style="color: #099;">65</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n_states</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="729" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="769" 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">

769

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC769" class="line" lang="python">    <span class="n" style="color: #333;">reverse_alphabet</span><span class="p">[</span><span class="n" style="color: #333;">missing_data</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">missing_char</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="729" 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">

729

</td>

<td class="diff-line-num new_line" data-linenumber="770" 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">

770

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC770" class="line" lang="python">    <span class="n" style="color: #333;">letter_to_state</span><span class="p">[</span><span class="n" style="color: #333;">missing_char</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">missing_data</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC730" class="line" lang="python">    <span class="n" style="color: #333;">reverse_alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">letter_to_state</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="731" 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">

731

</td>

<td class="diff-line-num new_line" data-linenumber="771" 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">

771

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="732" 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">

732

</td>

<td class="diff-line-num new_line" data-linenumber="772" 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">

772

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC772" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="733" 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">

733

</td>

<td class="diff-line-num new_line" data-linenumber="773" 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">

773

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC773" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">### construct gtr model</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="734" 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">

734

</td>

<td class="diff-line-num new_line" data-linenumber="774" 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">

774

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC774" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC735" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">        <span class="n" style="color: #333;">tmp_weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">t</span><span class="s" style="color: #d14;">'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weights</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 class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'tsv'</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">','</span><span class="p">,</span></span>

</pre>

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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="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC737" class="line" lang="python">                             <span class="n" style="color: #333;">skipinitialspace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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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="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">        <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ri</span><span class="p">,</span><span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp_weights</span><span class="p">.</span><span class="n" style="color: #333;">iterrows</span><span class="p">()}</span></span>

</pre>

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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="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">        <span class="n" style="color: #333;">mean_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()))</span></span>

</pre>

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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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<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC740" class="line" lang="python">        <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">weights</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">weights</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">mean_weight</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unique_states</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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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

</td>

<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC741" class="line" lang="python">        <span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">/=</span><span class="n" style="color: #333;">weights</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>

</pre>

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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

</td>

<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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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

</td>

<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="python">        <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="744" 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">

744

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<td class="diff-line-num new_line" data-linenumber="775" 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">

775

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC775" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="745" 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">

745

</td>

<td class="diff-line-num new_line" data-linenumber="776" 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">

776

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<pre style="margin: 0;"> <span id="LC776" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># set up dummy matrix</span></span>

</pre>

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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

</td>

<td class="diff-line-num new_line old" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC746" class="line" lang="python">    <span class="n" style="color: #333;">W</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ones</span><span class="p">((</span><span class="n" style="color: #333;">n<span class="idiff left">c</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">nc</span></span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="777" 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">

777

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC777" class="line" lang="python">    <span class="n" style="color: #333;">W</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ones</span><span class="p">((</span><span class="n" style="color: #333;">n<span class="idiff left">_states</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">n_states</span></span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="747" 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">

747

</td>

<td class="diff-line-num new_line" data-linenumber="778" 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">

778

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="748" 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">

748

</td>

<td class="diff-line-num new_line" data-linenumber="779" 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">

779

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC779" class="line" lang="python">    <span class="n" style="color: #333;">mugration_GTR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GTR</span><span class="p">.</span><span class="n" style="color: #333;">custom</span><span class="p">(</span><span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weights</span><span class="p">,</span> <span class="n" style="color: #333;">W</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">W</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

749

</td>

<td class="diff-line-num new_line old" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC749" class="line" lang="python">    <span class="n" style="color: #333;">mugration_GTR</span><span class="p">.</span><span class="n" style="color: #333;">profile_map</span><span class="p">[</span><span class="n" style="color: #333;">missing_char</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ones</span><span class="p">(</span><span class="n" style="color: #333;">n<span class="idiff left right">c</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC780" class="line" lang="python">    <span class="n" style="color: #333;">mugration_GTR</span><span class="p">.</span><span class="n" style="color: #333;">profile_map</span><span class="p">[</span><span class="n" style="color: #333;">missing_char</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ones</span><span class="p">(</span><span class="n" style="color: #333;">n<span class="idiff left right">_states</span></span><span class="p">)</span></span>

</pre>

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750

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<td class="diff-line-num new_line" data-linenumber="781" 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">

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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python">    <span class="n" style="color: #333;">mugration_GTR</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">missing_char</span></span>

</pre>

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751

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782

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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"></span>

</pre>

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752

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<td class="diff-line-num new_line" data-linenumber="783" 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">

783

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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"></span>

</pre>

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