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<h3 style="margin-top: 20px; margin-bottom: 10px;">

Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/phast">Debian Med / phast</a>

</h3>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

Commits:

</h4>

<ul>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363">204a70ae</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2024-12-06T21:26:04+01:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.7+dfsg</pre>

</li>

</ul>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

8 changed files:

</h4>

<ul>

<li class="file-stats">

<a href="#6840e7850dde729fc5d79094162595cb4659a605">

include/phast/fit_column.h

</a>

</li>

<li class="file-stats">

<a href="#0b53df8187ebc7ae01cff9b1b3897a1f9780e775">

src/dless/Makefile

</a>

</li>

<li class="file-stats">

<a href="#94fe7bf8cc252abcb08cbc0d97a0ca2b7ac1b90f">

src/lib/base/phast_misc.c

</a>

</li>

<li class="file-stats">

<a href="#572f6c814012863dc805b581a3b6434f21e38983">

src/lib/phylo/phast_fit_column.c

</a>

</li>

<li class="file-stats">

<a href="#1b5bfc86b125cb328b7d2c52ed1a87bc25a5134c">

src/lib/phylo/phast_fit_feature.c

</a>

</li>

<li class="file-stats">

<a href="#4fdff17600377a301fa7f7458a77748cb06a0e0f">

src/prequel/Makefile

</a>

</li>

<li class="file-stats">

<a href="#ece78a032e8effb46b4cccead2e1d42469704a62">

test/Makefile

</a>

</li>

<li class="file-stats">

<a href="#c63c88586c1127600684b4ff60d8706354cdf89b">

test/hmrc_summary_correct

</a>

</li>

</ul>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

Changes:

</h4>

<li id="6840e7850dde729fc5d79094162595cb4659a605">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#6840e7850dde729fc5d79094162595cb4659a605"><strong style="font-weight: 600;">include/phast/fit_column.h</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -143,9 +143,8 @@ double col_likelihood_wrapper_1d(double x, void *data);</td>

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<td class="new_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC143" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">  @note Uses log rather than log2</span></span>

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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC144" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">*/</span></span>

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<td class="new_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC145" class="line" lang="c"></span>

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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC146" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">TreeModel</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC147" class="line" lang="c">                                  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333333;">scratch</span><span class="p">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC148" class="line" lang="c"></span>

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<td class="old_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC146" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">col_compute_scaled_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">TreeModel</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC147" class="line" lang="c">                                                 <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333333;">scratch</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/** Compute and return the likelihood of a tree model with respect</span></span>

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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC149" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   to a single column tuple in an alignment.</span></span>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -229,7 +228,7 @@ double col_scale_derivs(ColFitData *d, double *first_deriv,</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC228" class="line" lang="c"></span>

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<td class="old_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC229" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/** Compute the first and (optionally) second derivatives with respect</span></span>

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<td class="old_line diff-line-num" data-linenumber="231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC230" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   to the scale parameters for the single-column log likelihood</span></span>

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<td class="old_line diff-line-num old" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC232" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   function (col_compute_log_likelihood).</span></span>

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<td class="old_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC231" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   function (col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood).</span></span>

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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC232" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   @param[in] d Column Data to analyze</span></span>

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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC233" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   @param[out] gradient gradient from first partial derivative</span></span>

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<td class="old_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC234" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   @param[out] hessian (optional) second order partial derivative</span></span>

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<li id="0b53df8187ebc7ae01cff9b1b3897a1f9780e775">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#0b53df8187ebc7ae01cff9b1b3897a1f9780e775"><strong style="font-weight: 600;">src/dless/Makefile</strong></a>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3,7 +3,7 @@ PHAST := ${PHAST}/..</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="make"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="make"><span class="c" style="color: #999988; font-style: italic;">#EXEC = $(addprefix ${BIN}/,$(notdir ${PWD}))</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">PROGS</span> <span class="o" style="font-weight: 600;">=</span> dless dlessP</span>

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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">MODULES</span> <span class="o" style="font-weight: 600;">=</span> bd_phylo_hmm</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">MODULES</span> <span class="o" style="font-weight: 600;">=</span> <span class="idiff left right addition" style="background-color: #c7f0d2;">phast_</span>bd_phylo_hmm</span>

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7

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">EXEC</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">$(</span>addprefix <span class="p">${</span>BIN<span class="p">}</span>/,<span class="p">${</span>PROGS<span class="p">})</span></span>

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8

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8

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="make"></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="make"><span class="c" style="color: #999988; font-style: italic;"># assume all *.c files are source</span></span>

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<br>

</li>

<li id="94fe7bf8cc252abcb08cbc0d97a0ca2b7ac1b90f">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#94fe7bf8cc252abcb08cbc0d97a0ca2b7ac1b90f"><strong style="font-weight: 600;">src/lib/base/phast_misc.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="495" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -495,6 +495,7 @@ double normalize_probs(double *p, int size) {</td>

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495

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC495" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">i</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

496

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC496" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span></span>

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497

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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC497" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span> <span class="n" style="color: #333333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">size</span><span class="p">;</span> <span class="n" style="color: #333333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;">p</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">];</span></span>

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<td class="old_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

498

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC498" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333333;">sum</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">sum</span><span class="p">;</span></span>

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498

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<td class="new_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

499

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC499" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span> <span class="n" style="color: #333333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">size</span><span class="p">;</span> <span class="n" style="color: #333333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333333;">p</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333333;">sum</span><span class="p">;</span>  </span>

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499

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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

500

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC500" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">sum</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC501" class="line" lang="c"><span class="p">}</span></span>

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<li id="572f6c814012863dc805b581a3b6434f21e38983">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#572f6c814012863dc805b581a3b6434f21e38983"><strong style="font-weight: 600;">src/lib/phylo/phast_fit_column.c</strong></a>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -14,6 +14,7 @@</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   perform single-base LRTs, score tests, phyloP, etc. */</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="c"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><stdlib.h></span></span>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><float.h></span></span>

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><phast/fit_column.h></span></span>

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><phast/sufficient_stats.h></span></span>

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><phast/tree_likelihoods.h></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -37,7 +38,7 @@</td>

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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   sufficient stats already available.  Note that this function uses</span></span>

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   natural log rather than log2.  This function does allow for rate</span></span>

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC40" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   variation. */</span></span>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">col_compute_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">TreeModel</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_log_</span>likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">TreeModel</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="c">                                  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333333;">scratch</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="c"></span>

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">i</span><span class="p">,</span> <span class="n" style="color: #333333;">j</span><span class="p">,</span> <span class="n" style="color: #333333;">k</span><span class="p">,</span> <span class="n" style="color: #333333;">nodeidx</span><span class="p">,</span> <span class="n" style="color: #333333;">rcat</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -46,15 +47,17 @@ double col_compute_likelihood(TreeModel *mod, MSA *msa, int tupleidx,</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">total_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

47

</td>

<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

48

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="c">  <span class="n" style="color: #333333;">List</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">traversal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tr_postorder</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tree</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

48

</td>

<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

49

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333333;">pL</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

50

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">log_scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

51

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">scaling_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">DBL_MIN</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

49

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

52

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

50

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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

53

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tuple_size</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #009999;">1</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

51

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="c">    <span class="n" style="color: #333333;">die</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ERROR col_compute_likelihood: need tuple size 1, got %i</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

54

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="c">    <span class="n" style="color: #333333;">die</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ERROR col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_log_</span>likelihood: need tuple size 1, got %i</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

52

</td>

<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

55

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="c">       <span class="n" style="color: #333333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tuple_size</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

53

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

56

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC56" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">order</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #009999;">0</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

54

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<td class="new_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="c">    <span class="n" style="color: #333333;">die</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ERROR col_compute_likelihood: got mod->order of %i, expected 0</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

57

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="c">    <span class="n" style="color: #333333;">die</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ERROR col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_log_</span>likelihood: got mod->order of %i, expected 0</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

55

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<td class="new_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

58

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC58" class="line" lang="c">       <span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">order</span><span class="p">);</span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC59" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">allow_gaps</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="c">    <span class="n" style="color: #333333;">die</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ERROR col_compute_likelihood: need mod->allow_gaps to be TRUE</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="c">    <span class="n" style="color: #333333;">die</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ERROR col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_log_</span>likelihood: need mod->allow_gaps to be TRUE</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC61" class="line" lang="c"></span>

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC62" class="line" lang="c">  <span class="cm" style="color: #999988; font-style: italic;">/* allocate memory or use scratch if avail */</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC63" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">scratch</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -93,8 +96,14 @@ double col_compute_likelihood(TreeModel *mod, MSA *msa, int tupleidx,</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="c">          <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span> <span class="n" style="color: #333333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">nstates</span><span class="p">;</span> <span class="n" style="color: #333333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="c">            <span class="n" style="color: #333333;">totr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;">pL</span><span class="p">[</span><span class="n" style="color: #333333;">k</span><span class="p">][</span><span class="n" style="color: #333333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">rchild</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span></span>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC98" class="line" lang="c">              <span class="n" style="color: #333333;">mm_get</span><span class="p">(</span><span class="n" style="color: #333333;">rsubst_mat</span><span class="p">,</span> <span class="n" style="color: #333333;">i</span><span class="p">,</span> <span class="n" style="color: #333333;">k</span><span class="p">);</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="c"></span>

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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC97" class="line" lang="c">          <span class="n" style="color: #333333;">pL</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">][</span><span class="n" style="color: #333333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">totl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">totr</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC99" class="line" lang="c">          </span>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="c">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">totl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">totr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">scaling_threshold</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="c">            <span class="n" style="color: #333333;">pL</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">][</span><span class="n" style="color: #333333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333333;">totl</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333333;">scaling_threshold</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">totr</span><span class="p">;</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="c">            <span class="n" style="color: #333333;">log_scale</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333333;">log</span><span class="p">(</span><span class="n" style="color: #333333;">scaling_threshold</span><span class="p">);</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="c">          <span class="p">}</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC104" class="line" lang="c">          <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC105" class="line" lang="c">            <span class="n" style="color: #333333;">pL</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">][</span><span class="n" style="color: #333333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">totl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">totr</span><span class="p">;</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC106" class="line" lang="c">          <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC107" class="line" lang="c">        <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="c">    <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -110,20 +119,9 @@ double col_compute_likelihood(TreeModel *mod, MSA *msa, int tupleidx,</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC119" class="line" lang="c">    <span class="n" style="color: #333333;">sfree</span><span class="p">(</span><span class="n" style="color: #333333;">pL</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC120" class="line" lang="c">  <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC121" class="line" lang="c"></span>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333333;">total_prob</span><span class="p">);</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC114" class="line" lang="c"><span class="p">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC115" class="line" lang="c"></span>

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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC116" class="line" lang="c"></span>

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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

117

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC117" class="line" lang="c"></span>

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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

118

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* See col_compute_likelihood above for notes.</span></span>

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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

119

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC119" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   Note that this function uses natural log rather than log2</span></span>

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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC120" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>

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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

121

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">TreeModel</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

122

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="c">                                  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333333;">scratch</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

123

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">log</span><span class="p">(</span><span class="n" style="color: #333333;">col_compute_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span> <span class="n" style="color: #333333;">scratch</span><span class="p">));</span></span>

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<td class="old_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

122

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">log</span><span class="p">(</span><span class="n" style="color: #333333;">total_prob</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">log_scale</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

124

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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC123" class="line" lang="c"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC124" class="line" lang="c"></span>

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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="c"></span>

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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

127

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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

125

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC125" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* version of col_scale_derivs_subst that allows for the general case</span></span>

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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

128

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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC126" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   of complex eigenvalues and eigenvectors */</span></span>

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<td class="old_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC127" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">col_scale_derivs_subst_complex</span><span class="p">(</span><span class="n" style="color: #333333;">ColFitData</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">d</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -298,7 +296,7 @@ void col_scale_derivs_subst(ColFitData *d) {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="c"></span>

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<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Compute the first and (optionally) second derivatives with respect</span></span>

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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   to the scale parameter for the single-column log likelihood</span></span>

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<td class="old_line diff-line-num old" data-linenumber="301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

301

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<td class="new_line diff-line-num old" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC301" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   function (col_compute_log_likelihood).  This version assumes a</span></span>

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<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

299

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC299" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   function (col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood).  This version assumes a</span></span>

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<td class="old_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

302

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<td class="new_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC300" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   single scale parameter; see below for the subtree case.  Return</span></span>

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<td class="old_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC301" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   value is log likelihood, which is computed as a by-product.  Derivs</span></span>

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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC302" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   will be stored in *first_deriv and *second_deriv.  If second_deriv</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="447" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -449,7 +447,7 @@ double col_scale_derivs(ColFitData *d, double *first_deriv,</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC447" class="line" lang="c"></span>

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<td class="new_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC448" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Compute the first and (optionally) second derivatives with respect</span></span>

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451

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<td class="new_line diff-line-num" data-linenumber="449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

449

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC449" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   to the scale parameters for the single-column log likelihood</span></span>

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<td class="old_line diff-line-num old" data-linenumber="452" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

452

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<td class="new_line diff-line-num old" data-linenumber="450" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC452" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   function (col_compute_log_likelihood).  This version assumes scale</span></span>

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<td class="old_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="450" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC450" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   function (col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood).  This version assumes scale</span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC451" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   parameters for the whole tree and for the subtree.  Return value is</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC452" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   log likelihood, which is computed as a by-product.  Derivs will be</span></span>

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455

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC453" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   stored in *gradient and *hessian.  If hessian == NULL,</span></span>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -679,8 +677,8 @@ double col_likelihood_wrapper(Vector *params, void *data) {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC677" class="line" lang="c">  <span class="cm" style="color: #999988; font-style: italic;">/* reestimate subst models on edges */</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC678" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

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681

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC679" class="line" lang="c"></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC682" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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683

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC683" class="line" lang="c">                                         <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC680" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC681" class="line" lang="c">                                         <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC684" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Wrapper for likelihood function for use in parameter estimation;</span></span>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -695,8 +693,8 @@ double col_likelihood_wrapper_1d(double x, void *data) {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC693" class="line" lang="c">  <span class="cm" style="color: #999988; font-style: italic;">/* reestimate subst models on edges */</span></span>

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696

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694

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC694" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

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697

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695

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC695" class="line" lang="c"></span>

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698

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<td class="new_line diff-line-num old" data-linenumber="696" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC698" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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699

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<td class="new_line diff-line-num old" data-linenumber="696" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC699" class="line" lang="c">                                         <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

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696

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC696" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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697

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC697" class="line" lang="c">                                         <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

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700

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC698" class="line" lang="c"><span class="p">}</span></span>

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701

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC699" class="line" lang="c"></span>

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702

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<td class="new_line diff-line-num" data-linenumber="700" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

700

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC700" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Wrapper for gradient function for use in parameter estimation */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="771" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -771,7 +769,7 @@ void col_lrts(TreeModel *mod, MSA *msa, mode_type mode, double *tuple_pvals,</td>

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771

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC769" class="line" lang="c">      <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

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772

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC770" class="line" lang="c"></span>

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773

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<td class="new_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

771

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC771" class="line" lang="c">      <span class="cm" style="color: #999988; font-style: italic;">/* compute log likelihoods under null and alt hypotheses */</span></span>

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774

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC774" class="line" lang="c">      <span class="n" style="color: #333333;">null_lnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">i</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

772

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC772" class="line" lang="c">      <span class="n" style="color: #333333;">null_lnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">i</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

775

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<td class="new_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

773

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC773" class="line" lang="c"></span>

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<td class="old_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

776

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<td class="new_line diff-line-num" data-linenumber="774" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

774

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC774" class="line" lang="c">      <span class="n" style="color: #333333;">vec_set</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">params</span><span class="p">,</span> <span class="mi" style="color: #009999;">0</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">init_scale</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="777" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

777

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<td class="new_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC775" class="line" lang="c">      <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">i</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1368,16 +1366,16 @@ void col_scale_derivs_num(ColFitData *d, double *first_deriv,</td>

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<td class="new_line diff-line-num" data-linenumber="1366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1366" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">orig_scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="1367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1367" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="1368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1368" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1371

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<td class="new_line diff-line-num old" data-linenumber="1369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1371" class="line" lang="c">  <span class="n" style="color: #333333;">lnl1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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1372

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<td class="new_line diff-line-num old" data-linenumber="1369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1372" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1369" class="line" lang="c">  <span class="n" style="color: #333333;">lnl1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1370" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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1373

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<td class="new_line diff-line-num" data-linenumber="1371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1371

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1371" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

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1374

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<td class="new_line diff-line-num" data-linenumber="1372" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1372" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1375" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1375

</td>

<td class="new_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1375" class="line" lang="c">  <span class="n" style="color: #333333;">lnl2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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1376

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<td class="new_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1376" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1377" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1373

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1373" class="line" lang="c">  <span class="n" style="color: #333333;">lnl2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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1374

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1374" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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1377

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<td class="new_line diff-line-num" data-linenumber="1375" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1375

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1375" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1378" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1378

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<td class="new_line diff-line-num" data-linenumber="1376" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1376

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1376" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1379

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<td class="new_line diff-line-num old" data-linenumber="1377" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1379" class="line" lang="c">  <span class="n" style="color: #333333;">lnl3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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1380

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</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1380" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1377" class="line" lang="c">  <span class="n" style="color: #333333;">lnl3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1378" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

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<td class="old_line diff-line-num" data-linenumber="1381" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1381

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<td class="new_line diff-line-num" data-linenumber="1379" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1379

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1379" class="line" lang="c">  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">first_deriv</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333333;">lnl2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">lnl3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="1382" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1382

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<td class="new_line diff-line-num" data-linenumber="1380" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1380

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1380" class="line" lang="c">  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">second_deriv</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333333;">lnl1</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">lnl2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">lnl3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333333;">DERIV_EPSILON</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="1383" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1383

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<td class="new_line diff-line-num" data-linenumber="1381" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1381

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1381" class="line" lang="c"><span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1391,37 +1389,37 @@ void col_scale_derivs_subtree_num(ColFitData *d, Vector *gradient,</td>

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1391

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<td class="new_line diff-line-num" data-linenumber="1389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1389

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1389" class="line" lang="c"></span>

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1392

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<td class="new_line diff-line-num" data-linenumber="1390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1390

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1390" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">);</span></span>

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1393

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<td class="new_line diff-line-num" data-linenumber="1391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1391" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1394

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<td class="new_line diff-line-num old" data-linenumber="1392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1394" class="line" lang="c">  <span class="n" style="color: #333333;">lnl00</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

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1395

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<td class="new_line diff-line-num old" data-linenumber="1392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1395" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1392

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1392" class="line" lang="c">  <span class="n" style="color: #333333;">lnl00</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1393" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">        </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1394" class="line" lang="c"></span>

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1395

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1395" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="1398" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1398

</td>

<td class="new_line diff-line-num" data-linenumber="1396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1396

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1396" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1399" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1399

</td>

<td class="new_line diff-line-num old" data-linenumber="1397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1399" class="line" lang="c">  <span class="n" style="color: #333333;">lnl0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1400" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1400

</td>

<td class="new_line diff-line-num old" data-linenumber="1397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1400" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1397

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1397" class="line" lang="c">  <span class="n" style="color: #333333;">lnl0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1398" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1398

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1398" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1401

</td>

<td class="new_line diff-line-num" data-linenumber="1399" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1399

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1399" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1402" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1402

</td>

<td class="new_line diff-line-num" data-linenumber="1400" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1400

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1400" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1403

</td>

<td class="new_line diff-line-num" data-linenumber="1401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1401

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1401" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale_sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale_sub</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1404

</td>

<td class="new_line diff-line-num" data-linenumber="1402" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1402

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1402" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1405

</td>

<td class="new_line diff-line-num old" data-linenumber="1403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1405" class="line" lang="c">  <span class="n" style="color: #333333;">lnl01</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1406

</td>

<td class="new_line diff-line-num old" data-linenumber="1403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1406" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1403

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1403" class="line" lang="c">  <span class="n" style="color: #333333;">lnl01</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1404

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1404" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">        </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="1407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1407

</td>

<td class="new_line diff-line-num" data-linenumber="1405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1405

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1405" class="line" lang="c"></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="1408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1408

</td>

<td class="new_line diff-line-num" data-linenumber="1406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1406

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1406" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1409

</td>

<td class="new_line diff-line-num" data-linenumber="1407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1407

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1407" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale_sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale_sub</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="1410" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1410

</td>

<td class="new_line diff-line-num" data-linenumber="1408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1408

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1408" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="1411" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1411

</td>

<td class="new_line diff-line-num old" data-linenumber="1409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1411" class="line" lang="c">  <span class="n" style="color: #333333;">lnl1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1412" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1412

</td>

<td class="new_line diff-line-num old" data-linenumber="1409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1412" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1409

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1409" class="line" lang="c">  <span class="n" style="color: #333333;">lnl1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1410" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1410

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1410" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1413

</td>

<td class="new_line diff-line-num" data-linenumber="1411" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1411

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1411" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1414

</td>

<td class="new_line diff-line-num" data-linenumber="1412" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1412

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1412" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1415

</td>

<td class="new_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1413

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1413" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale_sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale_sub</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1416" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1416

</td>

<td class="new_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1414

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1414" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="1417" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1417

</td>

<td class="new_line diff-line-num old" data-linenumber="1415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1417" class="line" lang="c">  <span class="n" style="color: #333333;">lnl11</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1418

</td>

<td class="new_line diff-line-num old" data-linenumber="1415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1418" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1415

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1415" class="line" lang="c">  <span class="n" style="color: #333333;">lnl11</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1416" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1416

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1416" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">        </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1419

</td>

<td class="new_line diff-line-num" data-linenumber="1417" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1417

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1417" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1420" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1420

</td>

<td class="new_line diff-line-num" data-linenumber="1418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1418

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1418" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1421

</td>

<td class="new_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1419

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1419" class="line" lang="c">  <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">scale_sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">orig_scale_sub</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1422" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1422

</td>

<td class="new_line diff-line-num" data-linenumber="1420" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1420

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1420" class="line" lang="c">  <span class="n" style="color: #333333;">tm_set_subst_matrices</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1423

</td>

<td class="new_line diff-line-num old" data-linenumber="1421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1423" class="line" lang="c">  <span class="n" style="color: #333333;">lnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1424

</td>

<td class="new_line diff-line-num old" data-linenumber="1421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1424" class="line" lang="c">                                    <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1421

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1421" class="line" lang="c">  <span class="n" style="color: #333333;">lnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tupleidx</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1422" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1422

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1422" class="line" lang="c">                                    <span class="idiff left right addition" style="background-color: #c7f0d2;">      </span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">fels_scratch</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1425

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<td class="new_line diff-line-num" data-linenumber="1423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1423

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1423" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1426

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<td class="new_line diff-line-num" data-linenumber="1424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1424

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1424" class="line" lang="c">  <span class="n" style="color: #333333;">gradient</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">data</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333333;">lnl0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">lnl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1427

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<td class="new_line diff-line-num" data-linenumber="1425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1425

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1425" class="line" lang="c">  <span class="n" style="color: #333333;">gradient</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">data</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333333;">lnl1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">lnl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333333;">DERIV_EPSILON</span><span class="p">;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1628" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1626" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1628,4 +1626,4 @@ int col_has_data_sub(TreeModel *mod, MSA *msa, int tupleidx, List *inside,</td>

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1628

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<td class="new_line diff-line-num" data-linenumber="1626" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1626" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">TRUE</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="1629" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1629

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<td class="new_line diff-line-num" data-linenumber="1627" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1627

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1627" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1630" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1630

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<td class="new_line diff-line-num" data-linenumber="1628" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1628" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">FALSE</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="1631" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1629" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1631" class="line" lang="c"><span class="p">}</span></span></pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1632" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1629" class="line" lang="c"><span class="p">}</span></span></pre></td>

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<li id="1b5bfc86b125cb328b7d2c52ed1a87bc25a5134c">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#1b5bfc86b125cb328b7d2c52ed1a87bc25a5134c"><strong style="font-weight: 600;">src/lib/phylo/phast_fit_feature.c</strong></a>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -25,15 +25,15 @@</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   parameters (currently affects 1d parameter estimation only) */</span></span>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="c"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Compute and return the log likelihood of a tree model with respect</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   to a given feature.  Calls col_compute_log_likelihood for each</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   to a given feature.  Calls col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood for each</span></span>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

29

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC29" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">   column */</span> </span>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="c"><span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">ff_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">TreeModel</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">GFF_Feature</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">feat</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="c">                                 <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333333;">scratch</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

33

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC33" class="line" lang="c">  <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">i</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

34

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC34" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">feat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">start</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">;</span> <span class="n" style="color: #333333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">feat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">end</span><span class="p">;</span> <span class="n" style="color: #333333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="cm" style="color: #999988; font-style: italic;">/* offset of one */</span></span>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="c">    <span class="n" style="color: #333333;">retval</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;">col_compute_log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tuple_idx</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">],</span> </span>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="c">                                         <span class="n" style="color: #333333;">scratch</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="c">    <span class="n" style="color: #333333;">retval</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;">col_compute_<span class="idiff left right addition" style="background-color: #c7f0d2;">scaled_</span>log_likelihood</span><span class="p">(</span><span class="n" style="color: #333333;">mod</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="p">,</span> <span class="n" style="color: #333333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">tuple_idx</span><span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">],</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="c">                                         <span class="idiff left right addition" style="background-color: #c7f0d2;">       </span><span class="n" style="color: #333333;">scratch</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">retval</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="c"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

39

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="c"></span>

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<li id="4fdff17600377a301fa7f7458a77748cb06a0e0f">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#4fdff17600377a301fa7f7458a77748cb06a0e0f"><strong style="font-weight: 600;">src/prequel/Makefile</strong></a>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3,7 +3,7 @@ PHAST := ${PHAST}/..</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="make"></span>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="make"><span class="c" style="color: #999988; font-style: italic;"># assume executable name is given by directory name</span></span>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

5

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">PROGS</span> <span class="o" style="font-weight: 600;">=</span> pbsDecode pbsEncode pbsScoreMatrix pbsTrain prequel</span>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">MODULES</span> <span class="o" style="font-weight: 600;">=</span> simplex_grid pbs_code</span>

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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">MODULES</span> <span class="o" style="font-weight: 600;">=</span> <span class="idiff left addition" style="background-color: #c7f0d2;">phast_</span>simplex_grid <span class="idiff right addition" style="background-color: #c7f0d2;">phast_</span>pbs_code</span>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">EXEC</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">$(</span>addprefix <span class="p">${</span>BIN<span class="p">}</span>/,<span class="p">${</span>PROGS<span class="p">})</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="make"></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="make"><span class="c" style="color: #999988; font-style: italic;"># assume all *.c files are source</span></span>

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<li id="ece78a032e8effb46b4cccead2e1d42469704a62">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#ece78a032e8effb46b4cccead2e1d42469704a62"><strong style="font-weight: 600;">test/Makefile</strong></a>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -7,30 +7,30 @@ all: msa_view phyloFit phastCons</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="make"><span class="nl">msa_view</span><span class="o" style="font-weight: 600;">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="make">     <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"*** Testing msa_view ***"</span></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="make">     msa_view hmrc.ss <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--end</span> 10000 <span class="o" style="font-weight: 600;">></span> hmrc.fa</span>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

10

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<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc.fa hmrc_correct.fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc.fa hmrc_correct.fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="make">    msa_view hmrc.fa <span class="nt" style="color: #000080;">-o</span> PHYLIP <span class="o" style="font-weight: 600;">></span> hmrc.ph</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="make">    msa_view hmrc.ph <span class="nt" style="color: #000080;">-i</span> PHYLIP <span class="o" style="font-weight: 600;">></span> hmrc.fa</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc.fa hmrc_correct.fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc.fa hmrc_correct.fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

14

</td>

<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

14

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="make">    msa_view hmrc.ph <span class="nt" style="color: #000080;">--out-format</span> MPM <span class="nt" style="color: #000080;">--in-format</span> PHYLIP <span class="o" style="font-weight: 600;">></span> hmrc.mpm</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

15

</td>

<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

15

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="make">    msa_view hmrc.mpm <span class="nt" style="color: #000080;">--in-format</span> MPM <span class="o" style="font-weight: 600;">></span> hmrc.fa</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc.fa hmrc_correct.fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc.fa hmrc_correct.fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

17

</td>

<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

17

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="make">    msa_view hmrc.fa <span class="nt" style="color: #000080;">-o</span> SS <span class="o" style="font-weight: 600;">></span> hmrc_short_a.ss</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

18

</td>

<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

18

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">--end</span> 10000 <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">-o</span> SS <span class="o" style="font-weight: 600;">></span> hmrc_short_b.ss</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="new_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_short_[ab].ss<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_short_[ab].ss <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

20

</td>

<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

20

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="make">    msa_view <span class="nt" style="color: #000080;">--seqs</span> human,cow hmrc_short_a.ss <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">-o</span> SS | msa_view - <span class="nt" style="color: #000080;">-i</span> SS <span class="o" style="font-weight: 600;">></span> hm_a.fa</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

21

</td>

<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

21

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="make">    msa_view <span class="nt" style="color: #000080;">--seqs</span> human,cow hmrc.fa <span class="o" style="font-weight: 600;">></span> hm_b.fa</span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hm_[ab].fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

22

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hm_[ab].fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

23

</td>

<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

23

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">--gap-strip</span> ANY <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">-o</span> SS | msa_view - <span class="nt" style="color: #000080;">-i</span> SS <span class="o" style="font-weight: 600;">></span> hmrc_nogaps_a.fa</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

24

</td>

<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

24

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">-i</span> SS | msa_view - <span class="nt" style="color: #000080;">--gap-strip</span> ANY <span class="o" style="font-weight: 600;">></span> hmrc_nogaps_b.fa</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_nogaps_[ab].fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

25

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_nogaps_[ab].fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

26

</td>

<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

26

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="make">    msa_view hmrc.fa <span class="nt" style="color: #000080;">--seqs</span> human,cow <span class="nt" style="color: #000080;">--gap-strip</span> ALL <span class="o" style="font-weight: 600;">></span> hm_a.fa</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

27

</td>

<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

27

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="make">    msa_view hmrc_short_a.ss <span class="nt" style="color: #000080;">--seqs</span> human,cow <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--gap-strip</span> ALL <span class="o" style="font-weight: 600;">></span> hm_b.fa</span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

28

</td>

<td class="new_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hm_[ab].fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

28

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hm_[ab].fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

29

</td>

<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

29

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC29" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">--start</span> 10000 <span class="nt" style="color: #000080;">--end</span> 20000 <span class="nt" style="color: #000080;">-i</span> SS <span class="o" style="font-weight: 600;">></span> hmrc_sub_a.fa</span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

30

</td>

<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

30

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">-i</span> SS | msa_view - <span class="nt" style="color: #000080;">--start</span> 10000 <span class="nt" style="color: #000080;">--end</span> 20000 <span class="o" style="font-weight: 600;">></span> hmrc_sub_b.fa</span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="new_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_sub_[ab].fa<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

31

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_sub_[ab].fa <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

32

</td>

<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

32

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">--summary</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="o" style="font-weight: 600;">></span> hmrc_summary</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

33

</td>

<td class="new_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> hmrc_summary hmrc_summary_correct<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> <span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">-b</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>hmrc_summary hmrc_summary_correct <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC34" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #dd1144;">"Passed all tests.</span><span class="se" style="color: #dd1144;">\n</span><span class="s2" style="color: #dd1144;">"</span></span>

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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> hmrc.ph hmrc.fa hmrc.mpm hmrc_short_[ab].ss hm_[ab].fa hmrc_nogaps_[ab].fa hmrc_sub_[ab].fa hmrc_summary</span>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="make"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -43,40 +43,40 @@ msa_view:</td>

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="make"><span class="nl">phyloFit</span><span class="o" style="font-weight: 600;">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"*** Testing phyloFit ***"</span></span>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> JC69 <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod jc.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"<span class="idiff deletion" style="background-color: #fac5cd;">ERROR"</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">;</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">exit </span></span><span class="idiff right deletion" style="background-color: #fac5cd;">1</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod jc.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"<span class="idiff addition" style="background-color: #c7f0d2;">Rounding errors found"</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">;</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> diff </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">-u</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> phyloFit.mod jc.mod</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> JC69 <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"((((human,chimp), (mouse,rat)), cow), chicken)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod jc.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

48

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod jc.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

49

</td>

<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

49

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> F81 <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

50

</td>

<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod f81.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

50

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod f81.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

51

</td>

<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

51

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC51" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> HKY85 <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

52

</td>

<td class="new_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod hky.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

52

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod hky.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

53

</td>

<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

53

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> REV <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

54

</td>

<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

55

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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

55

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> UNREST <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

56

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<td class="new_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod unrest.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod unrest.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

57

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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC57" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> HKY85 <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">-k</span> 4 <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

58

</td>

<td class="new_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod hky-dg.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod hky-dg.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

59

</td>

<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC59" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> REV <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">-k</span> 4 <span class="nt" style="color: #000080;">--quiet</span> </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

60

</td>

<td class="new_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-dg.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-dg.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC61" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> HKY85 <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--EM</span> <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

62

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<td class="new_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod hky-em.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod hky-em.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

63

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC63" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> REV <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--EM</span> <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

64

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<td class="new_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-em.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-em.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="make">    phyloFit hpmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> REV <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(hg16, (mm3,rn3), galGal2)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--gaps-as-bases</span> <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-gaps.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-gaps.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> REV <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--init-model</span> rev.mod <span class="nt" style="color: #000080;">--post-probs</span> <span class="nt" style="color: #000080;">--lnl</span> <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-lnl.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

69

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.postprob rev.postprob<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

68

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-lnl.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

69

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.postprob rev.postprob <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

70

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

70

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC70" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> REV <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"(human, (mouse,rat))"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

71

</td>

<td class="new_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-hmr.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

71

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-hmr.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

72

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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

72

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--seqs</span> human,mouse,rat <span class="nt" style="color: #000080;">--unordered</span> <span class="nt" style="color: #000080;">-o</span> SS <span class="o" style="font-weight: 600;">></span> hmr.ss</span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

73

</td>

<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

73

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="make">    phyloFit hmr.ss <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

74

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-hmr2.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  <span class="c" style="color: #999988; font-style: italic;"># FIXME: rev-hmr.mod and rev-hmr2.mod should be equal </span><span class="o" style="font-weight: 600;">(</span>eq freqs being obtained from all seqs<span class="o" style="font-weight: 600;">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

74

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-hmr2.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  <span class="c" style="color: #999988; font-style: italic;"># FIXME: rev-hmr.mod and rev-hmr2.mod should be equal </span><span class="o" style="font-weight: 600;">(</span>eq freqs being obtained from all seqs<span class="o" style="font-weight: 600;">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

75

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="make">    msa_view hmrc.ss <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--seqs</span> human,mouse <span class="nt" style="color: #000080;">--unordered</span> <span class="nt" style="color: #000080;">-o</span> SS <span class="o" style="font-weight: 600;">></span> hm.ss</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

76

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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="make">    phyloFit hm.ss <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

77

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-hm.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod rev-hm.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC78" class="line" lang="make">    phyloFit hmrc.ss <span class="nt" style="color: #000080;">--subst-mod</span> UNREST <span class="nt" style="color: #000080;">--tree</span> <span class="s2" style="color: #dd1144;">"((human, mouse), cow)"</span> <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--ancestor</span> cow <span class="nt" style="color: #000080;">--quiet</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

79

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<td class="new_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod unrest-cow-anc.mod<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> phyloFit.mod unrest-cow-anc.mod <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC80" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #dd1144;">"Passed all tests.</span><span class="se" style="color: #dd1144;">\n</span><span class="s2" style="color: #dd1144;">"</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC81" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> phyloFit.mod phyloFit.postprob hmr.ss hm.ss</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC82" class="line" lang="make"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -87,12 +87,12 @@ phyloFit:</td>

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC87" class="line" lang="make"><span class="nl">phastCons</span><span class="o" style="font-weight: 600;">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC88" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"*** Testing phastCons ***"</span></span>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC89" class="line" lang="make">    phastCons hpmrc.ss hpmrc-rev-dg-global.mod <span class="nt" style="color: #000080;">--nrates</span> 20 <span class="nt" style="color: #000080;">--transitions</span> .08,.008 <span class="nt" style="color: #000080;">--quiet</span> <span class="nt" style="color: #000080;">--viterbi</span> elements.bed <span class="nt" style="color: #000080;">--seqname</span> chr22 <span class="o" style="font-weight: 600;">></span> cons.dat</span>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> cons.dat cons_correct.dat<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

91

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<td class="new_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> elements.bed elements_correct.bed<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> cons.dat cons_correct.dat <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> elements.bed elements_correct.bed <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="make">    tree_doctor hpmrc-rev-dg-global.mod <span class="nt" style="color: #000080;">--prune</span> galGal2 <span class="o" style="font-weight: 600;">></span> hpmr.mod</span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="make">    phastCons hpmrc.ss hpmr.mod <span class="nt" style="color: #000080;">--nrates</span> 20 <span class="nt" style="color: #000080;">--transitions</span> .08,.008 <span class="nt" style="color: #000080;">--quiet</span> <span class="nt" style="color: #000080;">--viterbi</span> elements-4way.bed <span class="nt" style="color: #000080;">--seqname</span> chr22 <span class="o" style="font-weight: 600;">></span> cons-4way.dat</span>

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<td class="new_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC94" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> cons-4way.dat cons-4way_correct.dat<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

95

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<td class="new_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC95" class="line" lang="make">    <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">@</span></span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[[</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;">-n</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span>diff <span class="nt" style="color: #000080;">--brief</span> elements-4way.bed elements-4way_correct.bed<span class="sb" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">`</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]]</span></span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

94

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC94" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> cons-4way.dat cons-4way_correct.dat <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

95

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="make">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">!</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>diff <span class="nt" style="color: #000080;">--brief</span> elements-4way.bed elements-4way_correct.bed <span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #dd1144;">"ERROR"</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span>  </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

96

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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

96

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #dd1144;">"Passed all tests.</span><span class="se" style="color: #dd1144;">\n</span><span class="s2" style="color: #dd1144;">"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

97

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

97

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="make">    <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> cons.dat cons-4way.dat elements.bed elements-4way.bed hpmr.mod</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

98

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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

98

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC98" class="line" lang="make"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -110,7 +110,7 @@ phyloP:</td>

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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC110" class="line" lang="make">   phyloP <span class="nt" style="color: #000080;">--null</span> 10 phyloFit.mod <span class="o" style="font-weight: 600;">></span> phyloP_null_test.txt</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC111" class="line" lang="make">   phyloP <span class="nt" style="color: #000080;">-i</span> SS phyloFit.mod hmrc.ss <span class="o" style="font-weight: 600;">></span> phyloP_sph_test.txt</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC112" class="line" lang="make">   phyloP <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--method</span> LRT phyloFit.mod hmrc.ss <span class="o" style="font-weight: 600;">></span> phyloP_lrt_test.txt</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="make"><span class="idiff left right deletion" style="background-color: #fac5cd;">        </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">phyloP</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">SS</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">--method</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">LRT</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">--mode</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">CONACC</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">phyloFit.mod</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">hmrc.ss</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">phyloP_lrt_conacc_test.txt</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

113

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="make"><span class="idiff left right addition" style="background-color: #c7f0d2;">      </span>phyloP <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--method</span> LRT <span class="nt" style="color: #000080;">--mode</span> CONACC phyloFit.mod hmrc.ss <span class="o" style="font-weight: 600;">></span> phyloP_lrt_conacc_test.txt</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

114

</td>

<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

114

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC114" class="line" lang="make">   phyloP <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--method</span> GERP phyloFit.mod hmrc.ss <span class="o" style="font-weight: 600;">></span> phyloP_gerp_test.txt</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

115

</td>

<td class="new_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

115

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC115" class="line" lang="make">   phyloP <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--method</span> SCORE phyloFit.mod hmrc.ss <span class="o" style="font-weight: 600;">></span> phyloP_score_test.txt</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

116

</td>

<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

116

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC116" class="line" lang="make">   phyloP <span class="nt" style="color: #000080;">-i</span> SS <span class="nt" style="color: #000080;">--method</span> LRT <span class="nt" style="color: #000080;">--wig-scores</span> phyloFit.mod hmrc.ss <span class="o" style="font-weight: 600;">></span> phyloP_wig_test.wig</span>

</pre></td>

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</table>

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<li id="c63c88586c1127600684b4ff60d8706354cdf89b">

<a href="https://salsa.debian.org/med-team/phast/-/commit/204a70aefa32de527b3f334bb1ff846ea8f69363#c63c88586c1127600684b4ff60d8706354cdf89b"><strong style="font-weight: 600;">test/hmrc_summary_correct</strong></a>

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<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">descrip.                     A         C         G         T       G+C    length  all_gaps some_gaps</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

2

</td>

<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="plaintext">descrip.                      A          C          G          T        G+C     length   all_gaps  some_gaps</span>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">hmrc.ss                 0.3258    0.1913    0.1827    0.3001    0.3740     95927         0     82185</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

5

</td>

<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

2

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext">hmrc.ss                 0.3258     0.1913     0.1827     0.3001     0.3740      95927          0      82185</span></pre></td>

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