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GitLab

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<h3>

Nilesh Patra pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-dendropy/-/commit/63174079f462f65ff253d2eefbd059d39a19a5a4">63174079</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-04-21T12:47:07+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.5.2</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-dendropy/-/commit/1920036b8ab6c57d2f9dda9d4140d63da9f0b4d8">1920036b</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-04-21T12:47:54+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/4.5.2'

Update to upstream version '4.5.2'

with Debian dir 6337e6b9af26aefd994911d020a6a7db1b6e1e8e</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-dendropy/-/commit/5b247c8ea28815480cac295345063878a61dbf30">5b247c8e</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-04-21T12:50:26+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-dendropy/-/commit/6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81">6f1153b5</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-04-21T12:51:11+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry

</pre>

</li>

</ul>

<h4>14 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

PKG-INFO

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

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<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

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<li class="file-stats">

<a href="#a6df77779a57766a7697e1102ef47a786c3d9acc">

src/DendroPy.egg-info/PKG-INFO

</a>

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<li class="file-stats">

<a href="#8ae0a97e2467c839aa9ca2c82b87133de5d4d388">

src/DendroPy.egg-info/SOURCES.txt

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<li class="file-stats">

<a href="#3b7fe512bdc492a284ca27e1127ed87c79dd3005">

src/dendropy/__init__.py

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<li class="file-stats">

<a href="#a2967e01ffdf35cc6ae0ada3dabcfe498dea2129">

src/dendropy/dataio/ioservice.py

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<li class="file-stats">

<a href="#23234c686ec59288baeb421b224a73e3428e63d6">

src/dendropy/dataio/nexusprocessing.py

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<a href="#889003962bb4d3a34822163a2c64564693bfc3b0">

src/dendropy/dataio/nexusreader.py

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<li class="file-stats">

<a href="#bbacab3414435cb5b8ccf8d4ef88cf0cf12d0d45">

src/dendropy/datamodel/basemodel.py

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<li class="file-stats">

<a href="#fda490e722a6fcaf9d5d18eb6ba85ad59ec8182d">

src/dendropy/model/birthdeath.py

</a>

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<li class="file-stats">

<a href="#5bcbb0b63c583b534287f2c47d06e39cbde64d01">

src/dendropy/model/protractedspeciation.py

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<li class="file-stats">

<a href="#2b98aed557dd248628ac8cf42ec071f41934db26">

<span class="new-file">

+

tests/data/trees/pythonidae.lower.mle.nex

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<li class="file-stats">

<a href="#f07a50deefbad92586a94e92793c506a2350c0b8">

<span class="new-file">

+

tests/data/trees/pythonidae.upper.mle.nex

</span>

</a>

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</ul>

<h4>Changes:</h4>

<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: DendroPy</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 4.5.<span class="idiff left right">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 4.5.<span class="idiff left right">2</span></span>

</pre>

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4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://packages.python.org/DendroPy/</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Jeet Sukumaran and Mark T. Holder</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,7 +65,7 @@ Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">        Current Release</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">        ===============</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">        </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">        The current release of DendroPy is version 4.5.<span class="idiff left right">1</span>.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">        The current release of DendroPy is version 4.5.<span class="idiff left right">2</span>.</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">        </span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">        </span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics</span>

</pre>

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</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-dendropy (4.5.2-1) UNRELEASED; urgency=medium</span>

</pre>

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

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team Upload.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version 4.5.2</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Declare compliance with policy 4.5.1</span>

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

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org>  Wed, 21 Apr 2021 12:48:39 +0530</span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">python-dendropy (4.5.1-1) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  [ Nilesh Patra ]</span>

</pre>

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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),</td>

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

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               python3-all,</span>

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               python3-setuptools</span>

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11

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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>

</pre>

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12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-dendropy</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-dendropy.git</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://dendropy.org/</span>

</pre>

</td>

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</li>

<li id="a6df77779a57766a7697e1102ef47a786c3d9acc">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#a6df77779a57766a7697e1102ef47a786c3d9acc"><strong>src/DendroPy.egg-info/PKG-INFO</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: DendroPy</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 4.5.<span class="idiff left right">1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 4.5.<span class="idiff left right">2</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://packages.python.org/DendroPy/</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Jeet Sukumaran and Mark T. Holder</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,7 +65,7 @@ Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">        Current Release</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">        ===============</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">        </span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">        The current release of DendroPy is version 4.5.<span class="idiff left right">1</span>.</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">        The current release of DendroPy is version 4.5.<span class="idiff left right">2</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">        </span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">        </span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics</span>

</pre>

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<br>

</li>

<li id="8ae0a97e2467c839aa9ca2c82b87133de5d4d388">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#8ae0a97e2467c839aa9ca2c82b87133de5d4d388"><strong>src/DendroPy.egg-info/SOURCES.txt</strong></a>

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="plaintext">tests/data/trees/pythonidae.annotated.nexml</span>

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<pre style="margin: 0;"> <span id="LC626" class="line" lang="plaintext">tests/data/trees/pythonidae.beast.mcmc.trees</span>

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="plaintext">tests/data/trees/pythonidae.beast.summary.tre</span>

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext">tests/data/trees/pythonidae.lower.mle.nex</span>

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="plaintext">tests/data/trees/pythonidae.mb.con</span>

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="plaintext">tests/data/trees/pythonidae.mb.run1.t</span>

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="plaintext">tests/data/trees/pythonidae.mb.run2.t</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="plaintext">tests/data/trees/pythonidae.reference-trees.no-taxa-block.nexus</span>

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644

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<td class="new_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC645" class="line" lang="plaintext">tests/data/trees/pythonidae.reference-trees.no-taxa-no-translate-block.nexus</span>

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="plaintext">tests/data/trees/pythonidae.reference-trees.taxon-numbers-only.newick</span>

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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext">tests/data/trees/pythonidae.upper.mle.nex</span>

</pre>

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="plaintext">tests/data/trees/rana.trees.nexus</span>

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<pre style="margin: 0;"> <span id="LC649" class="line" lang="plaintext">tests/data/trees/treebase_s373.xml</span></pre>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

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<li id="3b7fe512bdc492a284ca27e1127ed87c79dd3005">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#3b7fe512bdc492a284ca27e1127ed87c79dd3005"><strong>src/dendropy/__init__.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,7 +104,7 @@ from dendropy.legacy import treesum</td>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">## PACKAGE METADATA</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="n" style="color: #333;">__project__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DendroPy"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"4.5.<span class="idiff left right">1</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"4.5.<span class="idiff left right">2</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Jeet Sukumaran and Mark T. Holder"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder."</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"><span class="n" style="color: #333;">__citation__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Sukumaran, J and MT Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571."</span></span>

</pre>

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</li>

<li id="a2967e01ffdf35cc6ae0ada3dabcfe498dea2129">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#a2967e01ffdf35cc6ae0ada3dabcfe498dea2129"><strong>src/dendropy/dataio/ioservice.py</strong></a>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.datamodel</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">basemodel</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.datamodel</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">taxonmodel</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deprecate</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">textprocessing</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># ``product`` is a namedtuple("DataReaderProducts", ["taxon_namespaces", "tree_lists", "char_matrices"])</span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### Put this here as a way to propagate annotations from main file to trees, chars;</span></span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### Removed it because not sure if we should actually do this (metadata may not apply).</span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### For now, if we want to pull metadata from main file, we need to read as dataset and extract from there</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if global_annotations_target is None:</span></span>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     global_annotations_target = basemodel.Annotable()</span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     is_post_process_global_annotations = True</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># else:</span></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     is_post_process_global_annotations = False</span></span>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python">        <span class="n" style="color: #333;">product</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_read</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stream</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python">                <span class="n" style="color: #333;">taxon_namespace_factory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxon_namespace_factory</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python">                <span class="n" style="color: #333;">tree_list_factory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tree_list_factory</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">                <span class="n" style="color: #333;">char_matrix_factory</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python">                <span class="n" style="color: #333;">state_alphabet_factory</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python">                <span class="n" style="color: #333;">global_annotations_target</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">global_annotations_target</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if is_post_process_global_annotations:</span></span>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     for tree_list in product.tree_lists:</span></span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#         tree_list.copy_annotations_from(global_annotations_target)</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">product</span><span class="p">.</span><span class="n" style="color: #333;">tree_lists</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_char_matrices</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -369,12 +384,23 @@ class DataReader(IOService):</td>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">            <span class="n" style="color: #333;">char_matrix_factory</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">            <span class="n" style="color: #333;">state_alphabet_factory</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python">            <span class="n" style="color: #333;">global_annotations_target</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### Put this here as a way to propagate annotations from main file to trees, chars;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### Removed it because not sure if we should actually do this (metadata may not apply).</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### For now, if we want to pull metadata from main file, we need to read as dataset and extract from there</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if global_annotations_target is None:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     global_annotations_target = basemodel.Annotable()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     is_post_process_global_annotations = True</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># else:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     is_post_process_global_annotations = False</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">        <span class="n" style="color: #333;">product</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_read</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stream</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python">                <span class="n" style="color: #333;">taxon_namespace_factory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxon_namespace_factory</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python">                <span class="n" style="color: #333;">tree_list_factory</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python">                <span class="n" style="color: #333;">char_matrix_factory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">char_matrix_factory</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python">                <span class="n" style="color: #333;">state_alphabet_factory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">state_alphabet_factory</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">                <span class="n" style="color: #333;">global_annotations_target</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">global_annotations_target</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if is_post_process_global_annotations:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     for char_matrix in product.char_matrices:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#         char_matrix.copy_annotations_from(global_annotations_target)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">product</span><span class="p">.</span><span class="n" style="color: #333;">char_matrices</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">###############################################################################</span></span>

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</li>

<li id="23234c686ec59288baeb421b224a73e3428e63d6">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#23234c686ec59288baeb421b224a73e3428e63d6"><strong>src/dendropy/dataio/nexusprocessing.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,13 +40,13 @@ class NexusTokenizer(Tokenizer):</td>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">            <span class="n" style="color: #333;">preserve_unquoted_underscores</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">        <span class="n" style="color: #333;">Tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">            <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">src</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python">            <span class="n" style="color: #333;">uncaptured_delimiters</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">li</span>st</span><span class="p">(</span><span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\t\n\r</span><span class="s" style="color: #d14;">"</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python">            <span class="n" style="color: #333;">captured_delimiters</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">li</span>st</span><span class="p">(</span><span class="s" style="color: #d14;">"{}(),;:=</span><span class="se" style="color: #d14;">\\\"</span><span class="s" style="color: #d14;">"</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python">            <span class="n" style="color: #333;">quote_chars</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"'"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">            <span class="n" style="color: #333;">uncaptured_delimiters</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">s<span class="idiff left right">e</span>t</span><span class="p">(</span><span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\t\n\r</span><span class="s" style="color: #d14;">"</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">            <span class="n" style="color: #333;">captured_delimiters</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">s<span class="idiff left right">e</span>t</span><span class="p">(</span><span class="s" style="color: #d14;">"{}(),;:=</span><span class="se" style="color: #d14;">\\\"</span><span class="s" style="color: #d14;">"</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">            <span class="n" style="color: #333;">quote_chars</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"'"</span><span class="p"><span class="idiff right">)</span>,</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">            <span class="n" style="color: #333;">escape_quote_by_doubling</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python">            <span class="n" style="color: #333;">escape_chars</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python">            <span class="n" style="color: #333;">comment_begin</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"["</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python">            <span class="n" style="color: #333;">comment_end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"]"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">            <span class="n" style="color: #333;">escape_chars</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">""</span><span class="p"><span class="idiff right">)</span>,</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">            <span class="n" style="color: #333;">comment_begin</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"["</span><span class="p"><span class="idiff right">)</span>,</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">            <span class="n" style="color: #333;">comment_end</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"]"</span><span class="p"><span class="idiff right">)</span>,</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">            <span class="n" style="color: #333;">capture_comments</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">            <span class="n" style="color: #333;">preserve_unquoted_underscores</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">preserve_unquoted_underscores</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># self.preserve_unquoted_underscores = preserve_unquoted_underscores</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,38 +61,38 @@ class NexusTokenizer(Tokenizer):</td>

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

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">capture_eol</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">remove</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">discard</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

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

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">remove</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">discard</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">ppen</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">d</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" 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(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">ppen</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">d</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">remove</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">discard</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">remove</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">discard</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">ppen</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">d</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

87

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<td class="new_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">ppen</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">d</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_hyphens_as_captured_delimiters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">hyphens_as_captured_delimiters</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hyphens_as_captured_delimiters</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">ppen</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">a<span class="idiff left right">d</span>d</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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

95

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

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

<pre style="margin: 0;">-<span id="LC95" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">remove</span></span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">discard</span></span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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

<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>

</pre>

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<li id="889003962bb4d3a34822163a2c64564693bfc3b0">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#889003962bb4d3a34822163a2c64564693bfc3b0"><strong>src/dendropy/dataio/nexusreader.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -281,6 +281,11 @@ class NexusReader(ioservice.DataReader):</td>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;">        exclude_trees : bool</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;">            If |False|, then tree data will not be read. Defaults to</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;">            |True|: tree data will be read.</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;">        store_ignored_blocks : bool</span></span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"><span class="s" style="color: #d14;">            If |True|, then ignored NEXUS blocks will be stored under the annotation</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;">            (NOT attribute!) ``ignored_nexus_blocks''.</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;">            To dereference, for e.g.: ``dataset.annotations["ignored_nexus_blocks"]``.</span></span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to |False|: non-character and tree blocks will not be read.</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;">        attached_taxon_namespace : |TaxonNamespace|</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;">            Unify all operational taxonomic unit definitions in this namespace.</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;">        ignore_unrecognized_keyword_arguments : boolean, default: |False|</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -297,6 +302,7 @@ class NexusReader(ioservice.DataReader):</td>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># keyword validation scheme</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exclude_chars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"exclude_chars"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exclude_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"exclude_trees"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">store_ignored_blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"store_ignored_blocks"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_data_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"data_type"</span><span class="p">,</span> <span class="s" style="color: #d14;">"standard"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attached_taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"attached_taxon_namespace"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -336,6 +342,7 @@ class NexusReader(ioservice.DataReader):</td>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_char_matrices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tree_lists</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_product</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ignored_blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">## Reader Implementation</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -365,6 +372,16 @@ class NexusReader(ioservice.DataReader):</td>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python">                <span class="n" style="color: #333;">taxon_namespaces</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_taxon_namespaces</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">                <span class="n" style="color: #333;">tree_lists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tree_lists</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python">                <span class="n" style="color: #333;">char_matrices</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_char_matrices</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_global_annotations_target</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ignored_blocks</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python">            <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_global_annotations_target</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ignored_nexus_blocks"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_global_annotations_target</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">.</span><span class="n" style="color: #333;">add_new</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python">                        <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ignored_nexus_blocks"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python">                        <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ignored_blocks</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python">                        <span class="n" style="color: #333;">datatype_hint</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"xsd:list"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">                        <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python">                <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ignored_blocks</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_product</span></span>

</pre>

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369

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<td class="new_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

386

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

370

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<td class="new_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

387

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -590,7 +607,11 @@ class NexusReader(ioservice.DataReader):</td>

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590

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607

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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python">                        <span class="n" style="color: #333;">NexusReader</span><span class="p">.</span><span class="n" style="color: #333;">IncompleteBlockError</span><span class="p">)</span></span>

</pre>

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608

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

592

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<td class="new_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># unknown block</span></span>

</pre>

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593

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<td class="new_line diff-line-num old" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC593" class="line" lang="python">                <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_consume_to_end_of_block</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">token</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">store_ignored_blocks</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

611

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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python">                    <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_read_block_without_processing</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

612

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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ignored_blocks</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

613

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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python">                    <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_consume_to_end_of_block</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">###########################################################################</span></span>

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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">## TAXA BLOCK</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -640,19 +661,45 @@ class NexusReader(ioservice.DataReader):</td>

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python">            <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_taxon_namespace</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python">        <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">next_token</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Construct label lookup set</span></span>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># The get_taxon call is expensive for large taxon namespaces as it requires</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># a linear search. This causes significant performance penalties for loading</span></span>

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># very large trees into an empty taxon namespace as each new taxon requires</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># a worst case search of the existing namespace before it can be inserted.</span></span>

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># To alleviate this, we build a temporary one-time set of all the labels</span></span>

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<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># in the taxon namespace. Now we can determine in constant-time whether</span></span>

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># a label token corresponds to a new taxon that requires insertion,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC673" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># or if an existing taxon can be fetched with get_taxon.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python">        <span class="n" style="color: #333;">label_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([])</span></span>

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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">taxon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">_taxa</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">is_case_sensitive</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python">                <span class="n" style="color: #333;">label_set</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python">                <span class="n" style="color: #333;">label_set</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">lower_cased_label</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">';'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python">            <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token</span></span>

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<pre style="margin: 0;">-<span id="LC645" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># if taxon_namespace.has_taxon(label=label):</span></span>

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<pre style="margin: 0;">-<span id="LC646" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#     pass</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC647" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># elif len(taxon_namespace) >= self._file_specified_ntax and not self.attached_taxon_namespace:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#     raise self._too_many_taxa_error(taxon_namespace=taxon_namespace, label=label)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC649" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># else:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC650" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#     taxon_namespace.require_taxon(label=label)</span></span>

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python">            <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">get_taxon</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Convert the token to the appropriate case to check against label set</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">is_case_sensitive</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python">                <span class="n" style="color: #333;">check_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">label</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

688

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python">                <span class="n" style="color: #333;">check_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">label</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

689

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

690

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">check_label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">label_set</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

691

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python">                <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">get_taxon</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

692

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

653

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<td class="new_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file_specified_ntax</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attached_taxon_namespace</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">unconstrained_taxa_accumulation_mode</span><span class="p">:</span></span>

</pre>

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654

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<td class="new_line diff-line-num" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_too_many_taxa_error</span><span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

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<td class="new_line diff-line-num" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

695

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python">                <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">new_taxon</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

696

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

697

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Add the new label to the label lookup set too</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">is_case_sensitive</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

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

<pre style="margin: 0;">+<span id="LC699" class="line" lang="python">                    <span class="n" style="color: #333;">label_set</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python">                    <span class="n" style="color: #333;">label_set</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">lower_cased_label</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

702

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

<pre style="margin: 0;">+<span id="LC702" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<td class="new_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

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

<pre style="margin: 0;"> <span id="LC703" class="line" lang="python">            <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">next_token</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

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<td class="new_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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

<pre style="margin: 0;"> <span id="LC704" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">process_and_clear_comments_for_item</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">,</span></span>

</pre>

</td>

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658

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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">extract_comment_metadata</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1228,12 +1275,40 @@ class NexusReader(ioservice.DataReader):</td>

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<td class="old_line diff-line-num" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1228

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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1229

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<td class="new_line diff-line-num" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1276

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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="python">            <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DUMMY"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1230

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<td class="new_line diff-line-num" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1277

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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'END'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ENDBLOCK'</span><span class="p">)</span> \</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1231

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<td class="new_line diff-line-num old" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">is_eof</span><span class="p">()</span> \</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1232

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<td class="new_line diff-line-num old" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1232" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1278

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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="python">            <span class="idiff left right">    </span><span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">is_eof</span><span class="p">()</span> \</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1279

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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="python">            <span class="idiff left right">    </span><span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1233

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<td class="new_line diff-line-num" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1280

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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">skip_to_semicolon</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1234

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<td class="new_line diff-line-num" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1281

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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="python">            <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">next_token_ucase</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1235

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<td class="new_line diff-line-num" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1282

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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">token</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1236

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<td class="new_line diff-line-num" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1283

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

<pre style="margin: 0;"> <span id="LC1283" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1284

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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read_block_without_processing</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1285

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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># used for unknown blocks we want to save</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1286

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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># NOT (really) TESTED</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1287

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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Everybody else except Jeet: (REALLY) DO NOT USE!</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1288

</td>

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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Jeet: SORTA DO NOT USE WITHOUT MORE TESTING</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1289

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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">token</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1290

</td>

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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="python">            <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1291

</td>

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

<pre style="margin: 0;">+<span id="LC1291" class="line" lang="python">        <span class="n" style="color: #333;">block</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"BEGIN"</span><span class="p">,</span> <span class="n" style="color: #333;">token</span><span class="p">]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1292

</td>

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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="python">        <span class="n" style="color: #333;">old_uncaptured_delimiters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1293

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

<pre style="margin: 0;">+<span id="LC1293" class="line" lang="python">        <span class="n" style="color: #333;">old_captured_delimiters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1294

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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="python">        <span class="n" style="color: #333;">to_switch</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\r</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1295

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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ch</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_switch</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1296

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1297

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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1298

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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'END'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ENDBLOCK'</span><span class="p">)</span> \</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1299

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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="python">                <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">is_eof</span><span class="p">()</span> \</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1300

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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="python">                <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1301

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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="python">            <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">require_next_token</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1302

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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="python">            <span class="n" style="color: #333;">uctoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1303

</td>

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

<pre style="margin: 0;">+<span id="LC1303" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">uctoken</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"END"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">uctoken</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ENDBLOCK"</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1304

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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="python">                <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uctoken</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1305

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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="python">            <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1306

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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">uncaptured_delimiters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_uncaptured_delimiters</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1307

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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">captured_delimiters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_captured_delimiters</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1308

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

<pre style="margin: 0;">+<span id="LC1308" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_nexus_tokenizer</span><span class="p">.</span><span class="n" style="color: #333;">skip_to_semicolon</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># move past end</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1309

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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="python">        <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1310

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

<pre style="margin: 0;">+<span id="LC1310" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1311

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

<pre style="margin: 0;">+<span id="LC1311" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1237

</td>

<td class="new_line diff-line-num" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1312

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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read_character_states</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1238

</td>

<td class="new_line diff-line-num" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1313

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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="python">            <span class="n" style="color: #333;">character_data_vector</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1239

</td>

<td class="new_line diff-line-num" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1314

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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="python">            <span class="n" style="color: #333;">state_alphabet</span><span class="p">,</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="bbacab3414435cb5b8ccf8d4ef88cf0cf12d0d45">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#bbacab3414435cb5b8ccf8d4ef88cf0cf12d0d45"><strong>src/dendropy/datamodel/basemodel.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -632,6 +632,9 @@ class Annotable(object):</td>

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632

</td>

<td class="new_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"><span class="s" style="color: #d14;">    or other information as metadata should subclass.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

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<td class="new_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

634

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<td class="new_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

634

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

<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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

<pre style="margin: 0;">+<span id="LC636" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">comments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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

<pre style="margin: 0;">+<span id="LC637" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_annotations</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

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<td class="new_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"_annotations"</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_annotations</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AnnotationSet</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>

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<li id="fda490e722a6fcaf9d5d18eb6ba85ad59ec8182d">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#fda490e722a6fcaf9d5d18eb6ba85ad59ec8182d"><strong>src/dendropy/model/birthdeath.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -494,6 +494,509 @@ def birth_death_tree(birth_rate, death_rate, birth_rate_sd=0.0, death_rate_sd=0.</td>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python">            <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon</span></span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tree</span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#NICOLA: new version of birth-death tree simulation with linear time cost</span></span>

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#in number of tips instead of quadratic. To obtain this accelleration, however,</span></span>

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#I have removed variation in birth and death rates.</span></span>

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fast_birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#NICOLA: we are not allowing variation in birth and death rate so to have</span></span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#increased efficiency.</span></span>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python">    <span class="n" style="color: #333;">birth_rate_sd</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span></span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python">    <span class="n" style="color: #333;">death_rate_sd</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span></span>

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"><span class="s" style="color: #d14;">    Returns a birth-death tree with birth rate specified by ``birth_rate``, and</span></span>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"><span class="s" style="color: #d14;">    death rate specified by ``death_rate``, with edge lengths in continuous (real)</span></span>

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"><span class="s" style="color: #d14;">    units.</span></span>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"><span class="s" style="color: #d14;">    Tree growth is controlled by one or more of the following arguments, of which</span></span>

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"><span class="s" style="color: #d14;">    at least one must be specified:</span></span>

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"><span class="s" style="color: #d14;">        - If ``num_extant_tips`` is given as a keyword argument, tree is grown until the</span></span>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"><span class="s" style="color: #d14;">          number of EXTANT tips equals this number.</span></span>

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"><span class="s" style="color: #d14;">        - If ``num_extinct_tips`` is given as a keyword argument, tree is grown until the</span></span>

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"><span class="s" style="color: #d14;">          number of EXTINCT tips equals this number.</span></span>

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"><span class="s" style="color: #d14;">        - If ``num_total_tips`` is given as a keyword argument, tree is grown until the</span></span>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"><span class="s" style="color: #d14;">          number of EXTANT plus EXTINCT tips equals this number.</span></span>

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"><span class="s" style="color: #d14;">        - If 'max_time' is given as a keyword argument, tree is grown for</span></span>

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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"><span class="s" style="color: #d14;">          a maximum of ``max_time``.</span></span>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"><span class="s" style="color: #d14;">        - If ``gsa_ntax`` is given then the tree will be simulated up to this number of</span></span>

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"><span class="s" style="color: #d14;">          EXTANT tips (or 0 tips), then a tree will be randomly selected from the</span></span>

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"><span class="s" style="color: #d14;">          intervals which corresond to times at which the tree had exactly ``num_extant_tips``</span></span>

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"><span class="s" style="color: #d14;">          leaves. This allows for simulations according to the "General</span></span>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python"><span class="s" style="color: #d14;">          Sampling Approach" of Hartmann et al. (2010). If this option is</span></span>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python"><span class="s" style="color: #d14;">          specified, then ``num_extant_tips`` MUST be specified and</span></span>

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"><span class="s" style="color: #d14;">          ``num_extinct_tips`` and ``num_total_tips`` CANNOT be specified.</span></span>

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530

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python"></span>

</pre>

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531

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python"><span class="s" style="color: #d14;">    If more than one of the above is given, then tree growth will terminate when</span></span>

</pre>

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532

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python"><span class="s" style="color: #d14;">    *any* one of the termination conditions are met.</span></span>

</pre>

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533

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"></span>

</pre>

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534

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

</pre>

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535

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

536

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

537

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"><span class="s" style="color: #d14;">    birth_rate : float</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

538

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"><span class="s" style="color: #d14;">        The birth rate.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

539

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"><span class="s" style="color: #d14;">    death_rate : float</span></span>

</pre>

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540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"><span class="s" style="color: #d14;">        The death rate.</span></span>

</pre>

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541

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"><span class="s" style="color: #d14;">    birth_rate_sd : float</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"><span class="s" style="color: #d14;">        The standard deviation of the normally-distributed mutation added to</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"><span class="s" style="color: #d14;">        the birth rate as it is inherited by daughter nodes; if 0, birth rate</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

544

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"><span class="s" style="color: #d14;">        does not evolve on the tree.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"><span class="s" style="color: #d14;">    death_rate_sd : float</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

546

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"><span class="s" style="color: #d14;">        The standard deviation of the normally-distributed mutation added to</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

547

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"><span class="s" style="color: #d14;">        the death rate as it is inherited by daughter nodes; if 0, death rate</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

548

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

<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"><span class="s" style="color: #d14;">        does not evolve on the tree.</span></span>

</pre>

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549

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

550

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"><span class="s" style="color: #d14;">    Keyword Arguments</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"><span class="s" style="color: #d14;">    -----------------</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"><span class="s" style="color: #d14;">    num_extant_tips: int</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"><span class="s" style="color: #d14;">        If specified, branching process is terminated when number of EXTANT</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"><span class="s" style="color: #d14;">        tips equals this number.</span></span>

</pre>

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556

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"><span class="s" style="color: #d14;">    num_extinct_tips: int</span></span>

</pre>

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557

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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"><span class="s" style="color: #d14;">        If specified, branching process is terminated when number of EXTINCT</span></span>

</pre>

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558

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"><span class="s" style="color: #d14;">        tips equals this number.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

559

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"><span class="s" style="color: #d14;">    num_total_tips: int</span></span>

</pre>

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560

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"><span class="s" style="color: #d14;">        If specified, branching process is terminated when number of EXTINCT</span></span>

</pre>

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561

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"><span class="s" style="color: #d14;">        plus EXTANT tips equals this number.</span></span>

</pre>

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562

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"><span class="s" style="color: #d14;">    max_time: float</span></span>

</pre>

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563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"><span class="s" style="color: #d14;">        If specified, branching process is terminated when time reaches or</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

564

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"><span class="s" style="color: #d14;">        exceeds this value.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

565

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"><span class="s" style="color: #d14;">    gsa_ntax: int</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

566

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"><span class="s" style="color: #d14;">        The General Sampling Approach threshold for number of taxa. See above</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"><span class="s" style="color: #d14;">        for details.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

568

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"><span class="s" style="color: #d14;">    tree : Tree instance</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"><span class="s" style="color: #d14;">        If given, then this tree will be used; otherwise a new one will be created.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"><span class="s" style="color: #d14;">    taxon_namespace : TaxonNamespace instance</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"><span class="s" style="color: #d14;">        If given, then this will be assigned to the new tree, and, in addition,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"><span class="s" style="color: #d14;">        taxa assigned to tips will be sourced from or otherwise created with</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"><span class="s" style="color: #d14;">        reference to this.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"><span class="s" style="color: #d14;">    is_assign_extant_taxa : bool [default: True]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"><span class="s" style="color: #d14;">        If False, then taxa will not be assigned to extant tips. If True</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"><span class="s" style="color: #d14;">        (default), then taxa will be assigned to extant tips. Taxa will be</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"><span class="s" style="color: #d14;">        assigned from the specified ``taxon_namespace`` or</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"><span class="s" style="color: #d14;">        ``tree.taxon_namespace``. If the number of taxa required exceeds the</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"><span class="s" style="color: #d14;">        number of taxa existing in the taxon namespace, new |Taxon| objects</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"><span class="s" style="color: #d14;">        will be created as needed and added to the taxon namespace.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"><span class="s" style="color: #d14;">    is_assign_extinct_taxa : bool [default: True]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"><span class="s" style="color: #d14;">        If False, then taxa will not be assigned to extant tips. If True</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"><span class="s" style="color: #d14;">        (default), then taxa will be assigned to extant tips. Taxa will be</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"><span class="s" style="color: #d14;">        assigned from the specified ``taxon_namespace`` or</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"><span class="s" style="color: #d14;">        ``tree.taxon_namespace``. If the number of taxa required exceeds the</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"><span class="s" style="color: #d14;">        number of taxa existing in the taxon namespace, new |Taxon| objects</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"><span class="s" style="color: #d14;">        will be created as needed and added to the taxon namespace. Note that</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"><span class="s" style="color: #d14;">        this option only makes sense if extinct tips are retained (specified via</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"><span class="s" style="color: #d14;">        'is_retain_extinct_tips' option), and will otherwise be ignored.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"><span class="s" style="color: #d14;">    is_add_extinct_attr: bool [default: True]</span></span>

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"><span class="s" style="color: #d14;">        If True (default), add an boolean attribute indicating whether or not a</span></span>

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"><span class="s" style="color: #d14;">        node is an extinct tip or not. False will skip this. Name of attribute</span></span>

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"><span class="s" style="color: #d14;">        is set by 'extinct_attr_name' argument, defaulting to 'is_extinct'.</span></span>

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"><span class="s" style="color: #d14;">        Note that this option only makes sense if extinct tips are retained</span></span>

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"><span class="s" style="color: #d14;">        (specified via 'is_retain_extinct_tips' option), and will otherwise be</span></span>

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"><span class="s" style="color: #d14;">        ignored.</span></span>

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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"><span class="s" style="color: #d14;">    extinct_attr_name: str [default: 'is_extinct']</span></span>

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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"><span class="s" style="color: #d14;">        Name of attribute to add to nodes indicating whether or not tip is extinct.</span></span>

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"><span class="s" style="color: #d14;">        Note that this option only makes sense if extinct tips are retained</span></span>

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"><span class="s" style="color: #d14;">        (specified via 'is_retain_extinct_tips' option), and will otherwise be</span></span>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"><span class="s" style="color: #d14;">        ignored.</span></span>

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"><span class="s" style="color: #d14;">    is_retain_extinct_tips : bool [default: False]</span></span>

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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"><span class="s" style="color: #d14;">        If True, extinct tips will be retained on tree. Defaults to False:</span></span>

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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"><span class="s" style="color: #d14;">        extinct lineages removed from tree.</span></span>

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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"><span class="s" style="color: #d14;">    repeat_until_success: bool [default: True]</span></span>

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"><span class="s" style="color: #d14;">        Under some conditions, it is possible for all lineages on a tree to go</span></span>

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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"><span class="s" style="color: #d14;">        extinct. In this case, if this argument is given as |True| (the</span></span>

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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"><span class="s" style="color: #d14;">        default), then a new branching process is initiated. If |False|</span></span>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"><span class="s" style="color: #d14;">        (default), then a TreeSimTotalExtinctionException is raised.</span></span>

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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"><span class="s" style="color: #d14;">    rng: random.Random() or equivalent instance</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"><span class="s" style="color: #d14;">        A Random() object or equivalent can be passed using the ``rng`` keyword;</span></span>

</pre>

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612

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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"><span class="s" style="color: #d14;">        otherwise GLOBAL_RNG is used.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"><span class="s" style="color: #d14;">    References</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"><span class="s" style="color: #d14;">    Hartmann, Wong, and Stadler "Sampling Trees from Evolutionary Models" Systematic Biology. 2010. 59(4). 465-476</span></span>

</pre>

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618

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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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620

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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"assign_taxa"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>

</pre>

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621

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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python">        <span class="n" style="color: #333;">deprecate</span><span class="p">.</span><span class="n" style="color: #333;">dendropy_deprecation_warning</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

622

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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python">                <span class="n" style="color: #333;">message</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Deprecated: 'assign_taxa' will no longer be supported as an argument to this function. Use 'is_assign_extant_taxa' and/or 'is_assign_extinct_taxa' instead"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python">                <span class="n" style="color: #333;">stacklevel</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python">        <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"assign_taxa"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

625

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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"is_assign_extant_taxa"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

626

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"is_assign_extant_taxa"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"ntax"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python">        <span class="n" style="color: #333;">deprecate</span><span class="p">.</span><span class="n" style="color: #333;">dendropy_deprecation_warning</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python">                <span class="n" style="color: #333;">message</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Deprecated: 'ntax' is no longer supported as an argument to this function. Use one or more of the following instead: 'num_extant_tips', 'num_extinct_tips', 'num_total_tips', or 'max_time'"</span><span class="p">,</span></span>

</pre>

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630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python">                <span class="n" style="color: #333;">stacklevel</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"num_extant_tips"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"ntax"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="s" style="color: #d14;">"num_extant_tips"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">"num_extinct_tips"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">"num_total_tips"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">"max_time"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"taxon_namespace"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">### cannot support legacy approach, b/c ``taxon_namespace`` may grow during function, leading to unpredictable behavior</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># deprecate.dendropy_deprecation_warning(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#         preamble="Deprecated: The 'taxon_namespace' argument can no longer be used to specify a termination condition as a side-effect. Use one or more of the following instead with the length of the taxon namespace instance as a value: 'num_extant_tips', 'num_extinct_tips', or 'num_total_tips'",</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#         old_construct="tree = birth_death_tree(\n    ...\n    taxon_namespace=taxon_namespace,\n    ...\n)",</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#         new_construct="tree = birth_death_tree(\n    ...\n    taxon_namespace=taxon_namespace,\n    num_extant_tips=len(taxon_namespace),\n    ...\n)")</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC642" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># kwargs["num_extant_tips"] = len(kwargs["taxon_namespace"])</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"The 'taxon_namespace' argument can no longer be used to specify a termination condition as a side-effect."</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python">                             <span class="s" style="color: #d14;">"Use one or more of the following instead with the length of the taxon namespace instance as a value: "</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python">                             <span class="s" style="color: #d14;">"'num_extant_tips', 'num_extinct_tips', or 'num_total_tips'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC646" class="line" lang="python">                             <span class="s" style="color: #d14;">"That is, instead of:</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python">                             <span class="s" style="color: #d14;">"    tree = birth_death_tree(</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        taxon_namespace=taxon_namespace,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">    )</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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648

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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python">                             <span class="s" style="color: #d14;">"Use:</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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649

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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python">                             <span class="s" style="color: #d14;">"    ntax = len(taxon_namespace)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">    tree = birth_death_tree(</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        taxon_namespace=taxon_namespace,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        num_extant_tips=ntax,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">    )</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="python">                             <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Or (recommended):</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python">                             <span class="s" style="color: #d14;">"    tree = birth_death_tree(</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        taxon_namespace=taxon_namespace,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        num_extant_tips=100,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">        ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">    )</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python">                             <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Note that the taxon namespace instance size may grow during any particular call of the function depending on taxon assignment/creation settings, so"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python">                             <span class="s" style="color: #d14;">" for stable and predictable behavor it is important to take a snapshot of the desired taxon namespace size before any call of the function, or, better yet"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python">                             <span class="s" style="color: #d14;">" simply pass in a constant value."</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python">                             <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"One or more of the following must be specified: 'num_extant_tips', 'num_extinct_tips', or 'max_time'"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python">    <span class="n" style="color: #333;">target_num_extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"num_extant_tips"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python">    <span class="n" style="color: #333;">target_num_extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"num_extinct_tips"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python">    <span class="n" style="color: #333;">target_num_total_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"num_total_tips"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python">    <span class="n" style="color: #333;">max_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'max_time'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python">    <span class="n" style="color: #333;">gsa_ntax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'gsa_ntax'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python">    <span class="n" style="color: #333;">is_add_extinct_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_add_extinct_attr'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python">    <span class="n" style="color: #333;">extinct_attr_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'extinct_attr_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'is_extinct'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python">    <span class="n" style="color: #333;">is_retain_extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_retain_extinct_tips'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

666

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python">    <span class="n" style="color: #333;">is_assign_extant_taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_assign_extant_taxa'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

667

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python">    <span class="n" style="color: #333;">is_assign_extinct_taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_assign_extinct_taxa'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

668

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python">    <span class="n" style="color: #333;">repeat_until_success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'repeat_until_success'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

669

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

<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

670

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python">    <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"tree"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

671

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python">    <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"taxon_namespace"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

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

<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

673

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

<pre style="margin: 0;">+<span id="LC673" class="line" lang="python">    <span class="n" style="color: #333;">rng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'rng'</span><span class="p">,</span> <span class="n" style="color: #333;">GLOBAL_RNG</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

674

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

<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

675

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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python">    <span class="n" style="color: #333;">ignore_unrecognized_keyword_arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'ignore_unrecognized_keyword_arguments'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

676

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

<pre style="margin: 0;">+<span id="LC676" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kwargs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">ignore_unrecognized_keyword_arguments</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

677

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

<pre style="margin: 0;">+<span id="LC677" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unsupported keyword arguments: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()))</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

678

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

<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

679

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python">    <span class="n" style="color: #333;">terminate_at_full_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

680

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

<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

681

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

<pre style="margin: 0;">+<span id="LC681" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

682

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

<pre style="margin: 0;">+<span id="LC682" class="line" lang="python">        <span class="n" style="color: #333;">terminate_at_full_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

683

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># gsa_ntax = 1 + target_num_taxa</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

684

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">target_num_extant_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

685

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"If 'gsa_ntax' is specified, 'num_extant_tips' must be specified"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

686

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

<pre style="margin: 0;">+<span id="LC686" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">target_num_extinct_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

687

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"If 'gsa_ntax' is specified, 'num_extinct_tups' cannot be specified"</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

688

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

<pre style="margin: 0;">+<span id="LC688" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">target_num_total_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

689

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

<pre style="margin: 0;">+<span id="LC689" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"If 'gsa_ntax' is specified, 'num_total_tips' cannot be specified"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

690

</td>

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

<pre style="margin: 0;">+<span id="LC690" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

691

</td>

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

<pre style="margin: 0;">+<span id="LC691" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"'gsa_ntax' ({}) must be greater than 'num_extant_tips' ({})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span><span class="p">,</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">))</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

692

</td>

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

<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

693

</td>

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

<pre style="margin: 0;">+<span id="LC693" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># initialize tree</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

694

</td>

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

<pre style="margin: 0;">+<span id="LC694" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tree</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

695

</td>

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

<pre style="margin: 0;">+<span id="LC695" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

696

</td>

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

<pre style="margin: 0;">+<span id="LC696" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">taxon_namespace</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

697

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

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

<pre style="margin: 0;">+<span id="LC698" class="line" lang="python">            <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">taxon_namespace</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python">        <span class="n" style="color: #333;">extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

</td>

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

<pre style="margin: 0;">+<span id="LC700" class="line" lang="python">        <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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

<pre style="margin: 0;">+<span id="LC701" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

702

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

<pre style="margin: 0;">+<span id="LC702" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">_child_nodes</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

703

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

<pre style="margin: 0;">+<span id="LC703" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

704

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

<pre style="margin: 0;">+<span id="LC704" class="line" lang="python">                    <span class="n" style="color: #333;">extant_tips</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

705

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;">#NICOLA: the reason for this will become clear later</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

706

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

<pre style="margin: 0;">+<span id="LC706" class="line" lang="python">                    <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

</td>

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

<pre style="margin: 0;">+<span id="LC707" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

708

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

<pre style="margin: 0;">+<span id="LC708" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

</td>

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

<pre style="margin: 0;">+<span id="LC709" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

</td>

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

<pre style="margin: 0;">+<span id="LC710" class="line" lang="python">                    <span class="n" style="color: #333;">extinct_tips</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

</td>

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

<pre style="margin: 0;">+<span id="LC711" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

712

</td>

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

<pre style="margin: 0;">+<span id="LC712" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

713

</td>

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

<pre style="margin: 0;">+<span id="LC713" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

714

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python">                <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

716

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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

717

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python">            <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">TaxonNamespace</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python">        <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

719

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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python">        <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">is_rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

720

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python">        <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python">        <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birth_rate</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

722

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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python">        <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">death_rate</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

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<pre style="margin: 0;">+<span id="LC724" class="line" lang="python">            <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

725

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<pre style="margin: 0;">+<span id="LC725" class="line" lang="python">        <span class="n" style="color: #333;">extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

726

</td>

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<pre style="margin: 0;">+<span id="LC726" class="line" lang="python">        <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

727

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<pre style="margin: 0;">+<span id="LC727" class="line" lang="python">    <span class="n" style="color: #333;">initial_extant_tip_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

728

</td>

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

<pre style="margin: 0;">+<span id="LC728" class="line" lang="python">    <span class="n" style="color: #333;">initial_extinct_tip_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

729

</td>

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

<pre style="margin: 0;">+<span id="LC729" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#NICOLA: in case we need a restart, let's record the initial branch lengths.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

730

</td>

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

<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">    <span class="n" style="color: #333;">initial_lengths</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

731

</td>

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

<pre style="margin: 0;">+<span id="LC731" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">initial_extant_tip_set</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

732

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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python">        <span class="n" style="color: #333;">initial_lengths</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

733

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<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

734

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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python">    <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

736

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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># for the GSA simulations targetted_time_slices is a list of tuple</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

737

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

<pre style="margin: 0;">+<span id="LC737" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   the first element in the tuple is the duration of the amount</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

738

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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   that the simulation spent at the (targetted) number of taxa</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

739

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

<pre style="margin: 0;">+<span id="LC739" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   and a list of edge information. The list of edge information includes</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

740

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<pre style="margin: 0;">+<span id="LC740" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   a list of terminal edges in the tree and the length for that edge</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

741

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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   that marks the beginning of the time slice that corresponds to the</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

742

</td>

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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   targetted number of taxa.</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

743

</td>

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

<pre style="margin: 0;">+<span id="LC743" class="line" lang="python">    <span class="n" style="color: #333;">targetted_time_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

744

</td>

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

<pre style="margin: 0;">+<span id="LC744" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

745

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

<pre style="margin: 0;">+<span id="LC745" class="line" lang="python">    <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

746

</td>

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

<pre style="margin: 0;">+<span id="LC746" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

747

</td>

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<pre style="margin: 0;">+<span id="LC747" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_extant_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">:</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

748

</td>

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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#NICOLA: here and in the other cases, update the branch length so to</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

</td>

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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#represent the true branch length (explained better below).</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

</td>

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

<pre style="margin: 0;">+<span id="LC750" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

751

</td>

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

<pre style="margin: 0;">+<span id="LC751" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

</td>

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

<pre style="margin: 0;">+<span id="LC752" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

</td>

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

<pre style="margin: 0;">+<span id="LC753" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_extinct_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_num_extinct_tips</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

754

</td>

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

<pre style="margin: 0;">+<span id="LC754" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

755

</td>

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

<pre style="margin: 0;">+<span id="LC755" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

</td>

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

<pre style="margin: 0;">+<span id="LC756" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

757

</td>

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

<pre style="margin: 0;">+<span id="LC757" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_total_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_num_total_tips</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

758

</td>

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

<pre style="margin: 0;">+<span id="LC758" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

759

</td>

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

<pre style="margin: 0;">+<span id="LC759" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

760

</td>

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

<pre style="margin: 0;">+<span id="LC760" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

761

</td>

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

<pre style="margin: 0;">+<span id="LC761" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_time</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_time</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

762

</td>

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

<pre style="margin: 0;">+<span id="LC762" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

763

</td>

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

<pre style="margin: 0;">+<span id="LC763" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

764

</td>

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

<pre style="margin: 0;">+<span id="LC764" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

765

</td>

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

<pre style="margin: 0;">+<span id="LC765" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="p">:</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

766

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<pre style="margin: 0;">+<span id="LC766" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

767

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<pre style="margin: 0;">+<span id="LC767" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

768

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<pre style="margin: 0;">+<span id="LC768" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

769

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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

770

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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

771

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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># get vector of birth/death probabilities, and</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

772

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

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

773

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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#NICOLA: replaced this</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

774

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

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

775

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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#         event_nodes = []</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

776

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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#         for nd in extant_tips:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

777

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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             if not hasattr(nd, 'birth_rate'):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

778

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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                 nd.birth_rate = birth_rate</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

779

</td>

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<pre style="margin: 0;">+<span id="LC779" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             if not hasattr(nd, 'death_rate'):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

780

</td>

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<pre style="margin: 0;">+<span id="LC780" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                 nd.death_rate = death_rate</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

781

</td>

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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             event_rates.append(nd.birth_rate)</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

782

</td>

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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             event_nodes.append((nd, True)) # birth event = True</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

783

</td>

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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             event_rates.append(nd.death_rate)</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

784

</td>

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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             event_nodes.append((nd, False)) # birth event = False; i.e. death</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

785

</td>

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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

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<pre style="margin: 0;">+<span id="LC787" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># get total probability of any birth/death</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

788

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<pre style="margin: 0;">+<span id="LC788" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#rate_of_any_event = sum(event_rates)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

789

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<pre style="margin: 0;">+<span id="LC789" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#NICOLA: instead, assume that each node has the same birth and death rate, and sample</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

790

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<pre style="margin: 0;">+<span id="LC790" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#from the total rate and then sample one node at random from extant ones.</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

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<pre style="margin: 0;">+<span id="LC791" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#this has constant cost instead of linear in the number of extant taxa.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

792

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<pre style="margin: 0;">+<span id="LC792" class="line" lang="python">        <span class="n" style="color: #333;">rate_of_any_event</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">death_rate</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

793

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<pre style="margin: 0;">+<span id="LC793" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

794

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<pre style="margin: 0;">+<span id="LC794" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># waiting time based on above probability</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

795

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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python">        <span class="n" style="color: #333;">waiting_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">expovariate</span><span class="p">(</span><span class="n" style="color: #333;">rate_of_any_event</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

796

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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

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<pre style="margin: 0;">+<span id="LC797" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

798

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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python">                <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

799

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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python">                <span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

800

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<pre style="margin: 0;">+<span id="LC800" class="line" lang="python">            <span class="n" style="color: #333;">edge_and_start_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

</td>

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<pre style="margin: 0;">+<span id="LC801" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

802

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<pre style="margin: 0;">+<span id="LC802" class="line" lang="python">                <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

803

</td>

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#NICOLA: modified accordingly</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

804

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python">                <span class="n" style="color: #333;">edge_and_start_length</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">))</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

805

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="python">            <span class="n" style="color: #333;">targetted_time_slices</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">waiting_time</span><span class="p">,</span> <span class="n" style="color: #333;">edge_and_start_length</span><span class="p">))</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

806

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">terminate_at_full_tree</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#NICOLA: terminal update as before</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

808

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<pre style="margin: 0;">+<span id="LC808" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

809

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<pre style="margin: 0;">+<span id="LC809" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

810

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

811

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<pre style="margin: 0;">+<span id="LC811" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

812

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<pre style="margin: 0;">+<span id="LC812" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># add waiting time to nodes</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

813

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<pre style="margin: 0;">+<span id="LC813" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#Nicola: this is the part that makes it quadratic in ntax.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

814

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<pre style="margin: 0;">+<span id="LC814" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#instead, we use a trick of initializing nd.edge.length to the time of node creation,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

815

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<pre style="margin: 0;">+<span id="LC815" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># and then we update it to the correct branch length when the node is closed or simulations are terminated.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

816

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<pre style="margin: 0;">+<span id="LC816" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#for nd in extant_tips:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

817

</td>

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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#    try:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

818

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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#        nd.edge.length += waiting_time</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

819

</td>

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<pre style="margin: 0;">+<span id="LC819" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#    except TypeError:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

820

</td>

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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#        nd.edge.length = waiting_time</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

821

</td>

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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python">        <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">waiting_time</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

822

</td>

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<pre style="margin: 0;">+<span id="LC822" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

823

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<pre style="margin: 0;">+<span id="LC823" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if event occurs within time constraints</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

824

</td>

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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_time</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">max_time</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

825

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<pre style="margin: 0;">+<span id="LC825" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># normalize probability</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

826

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<pre style="margin: 0;">+<span id="LC826" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#for i in range(len(event_rates)):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

827

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<pre style="margin: 0;">+<span id="LC827" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#    event_rates[i] = event_rates[i]/rate_of_any_event</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

828

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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># select node/event and process</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

829

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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#nd, birth_event = probability.weighted_choice(event_nodes, event_rates, rng=rng)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#NICOLA: instead of sampling from a categorical distribution (requiring linear time in ntax)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

831

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<pre style="margin: 0;">+<span id="LC831" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#sample a random integer to represent the chosen taxon, and sample if birth or death event.</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

832

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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python">            <span class="n" style="color: #333;">taxI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

833

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<pre style="margin: 0;">+<span id="LC833" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">()</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">death_rate</span><span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

834

</td>

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<pre style="margin: 0;">+<span id="LC834" class="line" lang="python">                <span class="n" style="color: #333;">birth_event</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

835

</td>

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<pre style="margin: 0;">+<span id="LC835" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

836

</td>

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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python">                <span class="n" style="color: #333;">birth_event</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

837

</td>

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<pre style="margin: 0;">+<span id="LC837" class="line" lang="python">            <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extant_tips</span><span class="p">[</span><span class="n" style="color: #333;">taxI</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

838

</td>

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<pre style="margin: 0;">+<span id="LC838" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#extant_tips.remove(nd)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

839

</td>

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<pre style="margin: 0;">+<span id="LC839" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">birth_event</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

840

</td>

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<pre style="margin: 0;">+<span id="LC840" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

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841

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<pre style="margin: 0;">+<span id="LC841" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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842

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<pre style="margin: 0;">+<span id="LC842" class="line" lang="python">                <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">new_child</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

843

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<pre style="margin: 0;">+<span id="LC843" class="line" lang="python">                <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">new_child</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

844

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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python">                <span class="n" style="color: #333;">extant_tips</span><span class="p">[</span><span class="n" style="color: #333;">taxI</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">c1</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

845

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<pre style="margin: 0;">+<span id="LC845" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#NICOLA: we initialize branch lengths to total time;</span></span>

</pre>

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846

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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#this may not make sense at first, but when we are done with a node, we</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

847

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<pre style="margin: 0;">+<span id="LC847" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#update the branch length to the new current time minus the time of node creation</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

848

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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#which gives us the branch length. The advantage is that this takes linear time</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

849

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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#instead of quadratic.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

850

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<pre style="margin: 0;">+<span id="LC850" class="line" lang="python">                <span class="n" style="color: #333;">c1</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_time</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

851

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python">                <span class="n" style="color: #333;">c2</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_time</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

852

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python">                <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_time</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

853

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#c1.edge.length = 0</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

854

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#c2.edge.length = 0</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

855

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<pre style="margin: 0;">+<span id="LC855" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#NICOLA: here, for speed, we don't allow variation in birth rates.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

856

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#It could be possible to allow it, but it would take ntax*log(ntax) time,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

857

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#which wouldn't be bad, but it would also require a more complicated approach.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

858

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<pre style="margin: 0;">+<span id="LC858" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#c1.birth_rate = nd.birth_rate + rng.gauss(0, birth_rate_sd)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

859

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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#c1.death_rate = nd.death_rate + rng.gauss(0, death_rate_sd)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

860

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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#c2.birth_rate = nd.birth_rate + rng.gauss(0, birth_rate_sd)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

861

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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#c2.death_rate = nd.death_rate + rng.gauss(0, death_rate_sd)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

862

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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python">                <span class="n" style="color: #333;">c1</span><span class="p">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">birth_rate</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

863

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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python">                <span class="n" style="color: #333;">c1</span><span class="p">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">death_rate</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

864

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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python">                <span class="n" style="color: #333;">c2</span><span class="p">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">birth_rate</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

865

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<pre style="margin: 0;">+<span id="LC865" class="line" lang="python">                <span class="n" style="color: #333;">c2</span><span class="p">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">death_rate</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

866

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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#extant_tips.append(c1)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

867

</td>

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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python">                <span class="n" style="color: #333;">extant_tips</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c2</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

868

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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

869

</td>

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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">[</span><span class="n" style="color: #333;">taxI</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

870

</td>

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<pre style="margin: 0;">+<span id="LC870" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

871

</td>

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

<pre style="margin: 0;">+<span id="LC871" class="line" lang="python">                    <span class="n" style="color: #333;">extinct_tips</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

872

</td>

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

<pre style="margin: 0;">+<span id="LC872" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

873

</td>

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

<pre style="margin: 0;">+<span id="LC873" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

874

</td>

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

875

</td>

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># total extinction</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

876

</td>

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

<pre style="margin: 0;">+<span id="LC876" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

877

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<pre style="margin: 0;">+<span id="LC877" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">targetted_time_slices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

878

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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python">                            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

879

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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">repeat_until_success</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

880

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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python">                        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TreeSimTotalExtinctionException</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

881

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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># We are going to basically restart the simulation because</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

882

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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># the tree has gone extinct (without reaching the specified</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

883

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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># ntax)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

884

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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python">                    <span class="n" style="color: #333;">extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">initial_extant_tip_set</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

885

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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python">                    <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">initial_extinct_tip_set</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

886

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<pre style="margin: 0;">+<span id="LC886" class="line" lang="python">                    <span class="n" style="color: #333;">ndIndex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

887

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

<pre style="margin: 0;">+<span id="LC887" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

888

</td>

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

<pre style="margin: 0;">+<span id="LC888" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

889

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

<pre style="margin: 0;">+<span id="LC889" class="line" lang="python">                            <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

890

</td>

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

<pre style="margin: 0;">+<span id="LC890" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">clear_child_nodes</span><span class="p">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

891

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

<pre style="margin: 0;">+<span id="LC891" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;">#NICOLA: restore branch length to original value</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

892

</td>

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

<pre style="margin: 0;">+<span id="LC892" class="line" lang="python">                        <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">initial_lengths</span><span class="p">[</span><span class="n" style="color: #333;">ndIndex</span><span class="p">]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

893

</td>

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

<pre style="margin: 0;">+<span id="LC893" class="line" lang="python">                        <span class="n" style="color: #333;">ndIndex</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

894

</td>

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

<pre style="margin: 0;">+<span id="LC894" class="line" lang="python">                    <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

895

</td>

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

<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

896

</td>

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

<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

897

</td>

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

<pre style="margin: 0;">+<span id="LC897" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

898

</td>

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

<pre style="margin: 0;">+<span id="LC898" class="line" lang="python">        <span class="n" style="color: #333;">total_duration_at_target_n_tax</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

899

</td>

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

<pre style="margin: 0;">+<span id="LC899" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">targetted_time_slices</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

900

</td>

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

<pre style="margin: 0;">+<span id="LC900" class="line" lang="python">            <span class="n" style="color: #333;">total_duration_at_target_n_tax</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

901

</td>

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

<pre style="margin: 0;">+<span id="LC901" class="line" lang="python">        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">total_duration_at_target_n_tax</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

902

</td>

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

<pre style="margin: 0;">+<span id="LC902" class="line" lang="python">        <span class="n" style="color: #333;">selected_slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

903

</td>

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

<pre style="margin: 0;">+<span id="LC903" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">targetted_time_slices</span><span class="p">):</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

904

</td>

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

<pre style="margin: 0;">+<span id="LC904" class="line" lang="python">            <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

905

</td>

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

<pre style="margin: 0;">+<span id="LC905" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

906

</td>

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

<pre style="margin: 0;">+<span id="LC906" class="line" lang="python">                <span class="n" style="color: #333;">selected_slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

907

</td>

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

<pre style="margin: 0;">+<span id="LC907" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">selected_slice</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

908

</td>

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

<pre style="margin: 0;">+<span id="LC908" class="line" lang="python">        <span class="n" style="color: #333;">edges_at_slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">selected_slice</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

909

</td>

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

<pre style="margin: 0;">+<span id="LC909" class="line" lang="python">        <span class="n" style="color: #333;">last_waiting_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">selected_slice</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

910

</td>

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

<pre style="margin: 0;">+<span id="LC910" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

911

</td>

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

<pre style="margin: 0;">+<span id="LC911" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">prev_length</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">edges_at_slice</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

912

</td>

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

<pre style="margin: 0;">+<span id="LC912" class="line" lang="python">            <span class="n" style="color: #333;">daughter_nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">head_node</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

913

</td>

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

<pre style="margin: 0;">+<span id="LC913" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">daughter_nd</span><span class="p">.</span><span class="n" style="color: #333;">child_nodes</span><span class="p">():</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

914

</td>

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

<pre style="margin: 0;">+<span id="LC914" class="line" lang="python">                <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">_parent_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

915

</td>

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

<pre style="margin: 0;">+<span id="LC915" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

916

</td>

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

<pre style="margin: 0;">+<span id="LC916" class="line" lang="python">                    <span class="n" style="color: #333;">extinct_tips</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

917

</td>

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

<pre style="margin: 0;">+<span id="LC917" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

918

</td>

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

<pre style="margin: 0;">+<span id="LC918" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

919

</td>

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

<pre style="margin: 0;">+<span id="LC919" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

920

</td>

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

<pre style="margin: 0;">+<span id="LC920" class="line" lang="python">                    <span class="n" style="color: #333;">extant_tips</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

921

</td>

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

<pre style="margin: 0;">+<span id="LC921" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

922

</td>

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

<pre style="margin: 0;">+<span id="LC922" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

923

</td>

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

<pre style="margin: 0;">+<span id="LC923" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">desc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">preorder_iter</span><span class="p">():</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

924

</td>

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

<pre style="margin: 0;">+<span id="LC924" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

925

</td>

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

<pre style="margin: 0;">+<span id="LC925" class="line" lang="python">                        <span class="n" style="color: #333;">extant_tips</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">desc</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

926

</td>

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

<pre style="margin: 0;">+<span id="LC926" class="line" lang="python">                    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

927

</td>

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

<pre style="margin: 0;">+<span id="LC927" class="line" lang="python">                        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

928

</td>

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

<pre style="margin: 0;">+<span id="LC928" class="line" lang="python">            <span class="n" style="color: #333;">daughter_nd</span><span class="p">.</span><span class="n" style="color: #333;">clear_child_nodes</span><span class="p">()</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

929

</td>

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

<pre style="margin: 0;">+<span id="LC929" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

930

</td>

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

<pre style="margin: 0;">+<span id="LC930" class="line" lang="python">                <span class="n" style="color: #333;">extinct_tips</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

931

</td>

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

<pre style="margin: 0;">+<span id="LC931" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

932

</td>

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

<pre style="margin: 0;">+<span id="LC932" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

933

</td>

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

<pre style="margin: 0;">+<span id="LC933" class="line" lang="python">            <span class="n" style="color: #333;">extant_tips</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

934

</td>

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

<pre style="margin: 0;">+<span id="LC934" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

935

</td>

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

<pre style="margin: 0;">+<span id="LC935" class="line" lang="python">                <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

936

</td>

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

<pre style="margin: 0;">+<span id="LC936" class="line" lang="python">            <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_waiting_time</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

937

</td>

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

<pre style="margin: 0;">+<span id="LC937" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

938

</td>

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

<pre style="margin: 0;">+<span id="LC938" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_retain_extinct_tips</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

939

</td>

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

<pre style="margin: 0;">+<span id="LC939" class="line" lang="python">        <span class="n" style="color: #333;">processed_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

940

</td>

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

<pre style="margin: 0;">+<span id="LC940" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">):</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

941

</td>

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

<pre style="margin: 0;">+<span id="LC941" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">processed_nodes</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

942

</td>

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

<pre style="margin: 0;">+<span id="LC942" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

943

</td>

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

<pre style="margin: 0;">+<span id="LC943" class="line" lang="python">            <span class="n" style="color: #333;">processed_nodes</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

944

</td>

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

<pre style="margin: 0;">+<span id="LC944" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

945

</td>

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

<pre style="margin: 0;">+<span id="LC945" class="line" lang="python">                <span class="n" style="color: #333;">extinct_tips</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

946

</td>

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

<pre style="margin: 0;">+<span id="LC946" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

947

</td>

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

<pre style="margin: 0;">+<span id="LC947" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

948

</td>

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

<pre style="margin: 0;">+<span id="LC948" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">_child_nodes</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

949

</td>

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

<pre style="margin: 0;">+<span id="LC949" class="line" lang="python">            <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">parent_node</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">parent_node</span><span class="p">.</span><span class="n" style="color: #333;">_child_nodes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

950

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<pre style="margin: 0;">+<span id="LC950" class="line" lang="python">                <span class="n" style="color: #333;">nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">parent_node</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

951

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<pre style="margin: 0;">+<span id="LC951" class="line" lang="python">                <span class="n" style="color: #333;">processed_nodes</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

952

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<pre style="margin: 0;">+<span id="LC952" class="line" lang="python">            <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">prune_subtree</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_unifurcations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

953

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<pre style="margin: 0;">+<span id="LC953" class="line" lang="python">    <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">suppress_unifurcations</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

954

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

<pre style="margin: 0;">+<span id="LC954" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

955

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<pre style="margin: 0;">+<span id="LC955" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_assign_extant_taxa</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_assign_extinct_taxa</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

956

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<pre style="margin: 0;">+<span id="LC956" class="line" lang="python">        <span class="n" style="color: #333;">taxon_pool</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">t</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

957

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<pre style="margin: 0;">+<span id="LC957" class="line" lang="python">        <span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">taxon_pool</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

958

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<pre style="margin: 0;">+<span id="LC958" class="line" lang="python">        <span class="n" style="color: #333;">taxon_pool_labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">label</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_pool</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

959

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

<pre style="margin: 0;">+<span id="LC959" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

960

</td>

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

<pre style="margin: 0;">+<span id="LC960" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### ONLY works if in GSA sub-section we remove ALL extant and</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

961

</td>

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

<pre style="margin: 0;">+<span id="LC961" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### extinct nodes beyond time slice: expensive</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

962

</td>

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

<pre style="margin: 0;">+<span id="LC962" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### Furthermore, main reason to use this approach is to have different</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

963

</td>

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

<pre style="margin: 0;">+<span id="LC963" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### label prefixes for extinct vs. extant lineages, but the second time</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

964

</td>

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

<pre style="margin: 0;">+<span id="LC964" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### this function is called with the same taxon namespace or any time</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

965

</td>

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

<pre style="margin: 0;">+<span id="LC965" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### this function is called with a populated taxon namespace, that</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

966

</td>

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

<pre style="margin: 0;">+<span id="LC966" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">### aesthetic is lost.</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

967

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<pre style="margin: 0;">+<span id="LC967" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># node_pool_labels = ("T", "X")</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

968

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<pre style="margin: 0;">+<span id="LC968" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># for node_pool_idx, node_pool in enumerate((extant_tips, extinct_tips)):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

969

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<pre style="margin: 0;">+<span id="LC969" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#     for node_idx, nd in enumerate(node_pool):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

970

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<pre style="margin: 0;">+<span id="LC970" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#         if taxon_pool:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

971

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<pre style="margin: 0;">+<span id="LC971" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#             taxon = taxon_pool.pop()</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

972

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<pre style="margin: 0;">+<span id="LC972" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#         else:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

973

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<pre style="margin: 0;">+<span id="LC973" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#             taxon = taxon_namespace.require_taxon("{}{}".format(node_pool_labels[node_pool_idx], node_idx+1))</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

974

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<pre style="margin: 0;">+<span id="LC974" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#         nd.taxon = taxon</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

975

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<pre style="margin: 0;">+<span id="LC975" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#         assert not nd._child_nodes</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

976

</td>

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<pre style="margin: 0;">+<span id="LC976" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

977

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<pre style="margin: 0;">+<span id="LC977" class="line" lang="python">        <span class="n" style="color: #333;">tlabel_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

978

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<pre style="margin: 0;">+<span id="LC978" class="line" lang="python">        <span class="n" style="color: #333;">leaf_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

979

</td>

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<pre style="margin: 0;">+<span id="LC979" class="line" lang="python">        <span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

980

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<pre style="margin: 0;">+<span id="LC980" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd_idx</span><span class="p">,</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

981

</td>

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<pre style="margin: 0;">+<span id="LC981" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_assign_extant_taxa</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

982

</td>

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<pre style="margin: 0;">+<span id="LC982" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

983

</td>

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<pre style="margin: 0;">+<span id="LC983" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_assign_extant_taxa</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extinct_tips</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

984

</td>

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

<pre style="margin: 0;">+<span id="LC984" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

985

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<pre style="margin: 0;">+<span id="LC985" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_pool</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

986

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<pre style="margin: 0;">+<span id="LC986" class="line" lang="python">                <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_pool</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

987

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<pre style="margin: 0;">+<span id="LC987" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

988

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<pre style="margin: 0;">+<span id="LC988" class="line" lang="python">                <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

989

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<pre style="margin: 0;">+<span id="LC989" class="line" lang="python">                    <span class="n" style="color: #333;">tlabel_counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

990

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<pre style="margin: 0;">+<span id="LC990" class="line" lang="python">                    <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="n" style="color: #333;">tlabel_counter</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

991

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<pre style="margin: 0;">+<span id="LC991" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_pool_labels</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

992

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<pre style="margin: 0;">+<span id="LC992" class="line" lang="python">                        <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

993

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<pre style="margin: 0;">+<span id="LC993" class="line" lang="python">                <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">require_taxon</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

994

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<pre style="margin: 0;">+<span id="LC994" class="line" lang="python">                <span class="n" style="color: #333;">taxon_pool_labels</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

995

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<pre style="margin: 0;">+<span id="LC995" class="line" lang="python">            <span class="n" style="color: #333;">nd</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

996

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<pre style="margin: 0;">+<span id="LC996" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tree</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

997

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<pre style="margin: 0;">+<span id="LC997" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

998

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<pre style="margin: 0;">+<span id="LC998" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

999

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

<pre style="margin: 0;">+<span id="LC999" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

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<td class="new_line diff-line-num" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1000

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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">discrete_birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="p">,</span> <span class="n" style="color: #333;">birth_rate_sd</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate_sd</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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498

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<td class="new_line diff-line-num" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1001

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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

</td>

<td class="new_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1002

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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="python"><span class="s" style="color: #d14;">    Returns a birth-death tree with birth rate specified by ``birth_rate``, and</span></span>

</pre>

</td>

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<br>

</li>

<li id="5bcbb0b63c583b534287f2c47d06e39cbde64d01">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#5bcbb0b63c583b534287f2c47d06e39cbde64d01"><strong>src/dendropy/model/protractedspeciation.py</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -691,25 +691,27 @@ class ProtractedSpeciationProcess(object):</td>

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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># we do this here so that the (newest) tip lineages have the</span></span>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># waiting time to the next event branch lengths</span></span>

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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC695" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">min_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC696" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">max_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC697" class="line" lang="python">                <span class="n" style="color: #333;">lineage_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">min_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">max_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python">                <span class="n" style="color: #333;">has_lineage_count_requirements</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python">                        <span class="p">(</span><span class="n" style="color: #333;">num_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">num_extant_lineages</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python">                        <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">min_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_extant_lineages</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python">                        <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">max_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">max_extant_lineages</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python">                        <span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python">                    <span class="n" style="color: #333;">is_lineage_count_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python">                    <span class="n" style="color: #333;">is_lineage_count_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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698

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC699" class="line" lang="python">                <span class="n" style="color: #333;">lineage_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python">                <span class="n" style="color: #333;">has_lineage_count_requirements</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python">                <span class="n" style="color: #333;">is_lineage_count_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_extant_lineages</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ProcessFailedException</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC702" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC703" class="line" lang="python">                    <span class="p">(</span><span class="n" style="color: #333;">num_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">num_extant_lineages</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC704" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">min_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_extant_lineages</span><span class="p">))</span></span>

</pre>

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705

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<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC705" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">max_extant_lineages</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="n" style="color: #333;">num_incipient_species</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_orthospecies</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">max_extant_lineages</span><span class="p">))</span></span>

</pre>

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706

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<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC706" class="line" lang="python">                    <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC707" class="line" lang="python">                <span class="n" style="color: #333;">lineage_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC709" class="line" lang="python">                <span class="n" style="color: #333;">lineage_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num_extant_orthospecies</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">max_extant_orthospecies</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">min_extant_orthospecies</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">## note: very expensive operation to count orthospecies leaves!</span></span>

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<pre style="margin: 0;">-<span id="LC712" class="line" lang="python">                <span class="n" style="color: #333;">orthospecies_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">+<span id="LC713" class="line" lang="python">                <span class="n" style="color: #333;">has_orthospecies_count_requirements</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python">                <span class="n" style="color: #333;">is_orthospecies_count_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python">                <span class="n" style="color: #333;">final_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">uniform</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">waiting_time</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">                <span class="n" style="color: #333;">lineage_collection_snapshot</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">lineage</span><span class="p">.</span><span class="n" style="color: #333;">clone</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lineage</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_collection"</span><span class="p">],</span> <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_collection"</span><span class="p">])]</span></span>

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -737,66 +739,71 @@ class ProtractedSpeciationProcess(object):</td>

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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python">                                <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python">                        <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_tree"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage_tree</span></span>

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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python">                        <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"orthospecies_tree"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orthospecies_tree</span></span>

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<pre style="margin: 0;">-<span id="LC740" class="line" lang="python">                        <span class="n" style="color: #333;">orthospecies_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">is_</span>orthospecies_<span class="idiff right">count_</span>requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;"> <span id="LC743" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ProcessFailedException</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC744" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC745" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_extant_orthospecies</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">num_leaves</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_extant_orthospecies</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ProcessFailedException</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

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<pre style="margin: 0;"> <span id="LC747" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

746

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC746" class="line" lang="python">                <span class="n" style="color: #333;">orthospecies_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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747

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC747" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># add to current time</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

748

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC748" class="line" lang="python">            <span class="n" style="color: #333;">current_time</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">waiting_time</span></span>

</pre>

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

749

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC749" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Select event</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC750" class="line" lang="python">            <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probability</span><span class="p">.</span><span class="n" style="color: #333;">weighted_index_choice</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">event_rates</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC751" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>

</pre>

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752

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC752" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC753" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Splitting of new incipient species lineage from orthospecies lineage</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC754" class="line" lang="python">                <span class="n" style="color: #333;">parent_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">choice</span><span class="p">(</span><span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

755

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC755" class="line" lang="python">                <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC756" class="line" lang="python">                <span class="n" style="color: #333;">new_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_lineage</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC757" class="line" lang="python">                        <span class="n" style="color: #333;">lineage_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC758" class="line" lang="python">                        <span class="n" style="color: #333;">parent_lineage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_lineage</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC759" class="line" lang="python">                        <span class="n" style="color: #333;">origin_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC760" class="line" lang="python">                        <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC761" class="line" lang="python">                <span class="n" style="color: #333;">lineage_collection</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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762

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC762" class="line" lang="python">                <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

763

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC763" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

764

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC764" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Extinction of an orthospecies lineage</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

765

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC765" class="line" lang="python">                <span class="n" style="color: #333;">lineage_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

766

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC766" class="line" lang="python">                <span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">].</span><span class="n" style="color: #333;">extinction_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

767

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC767" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

768

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC768" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

769

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC769" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Splitting of new incipient species lineage from incipient lineage</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

770

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC770" class="line" lang="python">                <span class="n" style="color: #333;">parent_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">choice</span><span class="p">(</span><span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">)</span></span>

</pre>

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

771

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC771" class="line" lang="python">                <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

772

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC772" class="line" lang="python">                <span class="n" style="color: #333;">new_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_lineage</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

773

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC773" class="line" lang="python">                        <span class="n" style="color: #333;">lineage_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

774

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC774" class="line" lang="python">                        <span class="n" style="color: #333;">parent_lineage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_lineage</span><span class="p">,</span></span>

</pre>

</td>

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

775

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC775" class="line" lang="python">                        <span class="n" style="color: #333;">origin_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

776

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC776" class="line" lang="python">                        <span class="p">)</span></span>

</pre>

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

777

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC777" class="line" lang="python">                <span class="n" style="color: #333;">lineage_collection</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

778

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC778" class="line" lang="python">                <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

779

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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

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

780

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC780" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Completion of speciation</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

781

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC781" class="line" lang="python">                <span class="n" style="color: #333;">lineage_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

782

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python">                <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

783

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC783" class="line" lang="python">                <span class="n" style="color: #333;">lineage</span><span class="p">.</span><span class="n" style="color: #333;">speciation_completion_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

784

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC784" class="line" lang="python">                <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"species_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

785

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC785" class="line" lang="python">                <span class="n" style="color: #333;">lineage</span><span class="p">.</span><span class="n" style="color: #333;">species_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"species_id"</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

786

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC786" class="line" lang="python">                <span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

787

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

788

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

789

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC789" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Extinction of an incipient_species lineage</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

790

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC790" class="line" lang="python">                <span class="n" style="color: #333;">lineage_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

791

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python">                <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">].</span><span class="n" style="color: #333;">extinction_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

792

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC792" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC793" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

794

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC794" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Unexpected event type index: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">event_type_idx</span><span class="p">))</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

795

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC795" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineage_requirements_met</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">orthospecies_requirements_met</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

748

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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python">                <span class="n" style="color: #333;">has_orthospecies_count_requirements</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python">                <span class="n" style="color: #333;">is_orthospecies_count_requirements_met</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

751

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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python">                    <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">has_lineage_count_requirements</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is_lineage_count_requirements_met</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">has_orthospecies_count_requirements</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is_orthospecies_count_requirements_met</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">has_lineage_count_requirements</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is_lineage_count_requirements_met</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">has_orthospecies_count_requirements</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">has_lineage_count_requirements</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">has_orthospecies_count_requirements</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is_orthospecies_count_requirements_met</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

754

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python">                <span class="n" style="color: #333;">final_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">uniform</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">waiting_time</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

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<td class="new_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

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<pre style="margin: 0;"> <span id="LC756" class="line" lang="python">                <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"final_time"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">final_time</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

798

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<td class="new_line diff-line-num old" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC798" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"OK"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="new_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

758

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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

759

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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># add to current time</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

760

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<pre style="margin: 0;">+<span id="LC760" class="line" lang="python">                <span class="n" style="color: #333;">current_time</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">waiting_time</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

761

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

<pre style="margin: 0;">+<span id="LC761" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Select event</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

762

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

<pre style="margin: 0;">+<span id="LC762" class="line" lang="python">                <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probability</span><span class="p">.</span><span class="n" style="color: #333;">weighted_index_choice</span><span class="p">(</span><span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">event_rates</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

763

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<pre style="margin: 0;">+<span id="LC763" class="line" lang="python">                <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

764

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<pre style="margin: 0;">+<span id="LC764" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

765

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<pre style="margin: 0;">+<span id="LC765" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Splitting of new incipient species lineage from orthospecies lineage</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

766

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<pre style="margin: 0;">+<span id="LC766" class="line" lang="python">                    <span class="n" style="color: #333;">parent_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">choice</span><span class="p">(</span><span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

767

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<pre style="margin: 0;">+<span id="LC767" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

768

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<pre style="margin: 0;">+<span id="LC768" class="line" lang="python">                    <span class="n" style="color: #333;">new_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_lineage</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

769

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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python">                            <span class="n" style="color: #333;">lineage_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">],</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

770

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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python">                            <span class="n" style="color: #333;">parent_lineage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_lineage</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

771

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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python">                            <span class="n" style="color: #333;">origin_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

772

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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python">                            <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

773

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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_collection</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

774

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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python">                    <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

775

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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

776

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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Extinction of an orthospecies lineage</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

777

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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

778

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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python">                    <span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">].</span><span class="n" style="color: #333;">extinction_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

779

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<pre style="margin: 0;">+<span id="LC779" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

780

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<pre style="margin: 0;">+<span id="LC780" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

781

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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Splitting of new incipient species lineage from incipient lineage</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

782

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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python">                    <span class="n" style="color: #333;">parent_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">choice</span><span class="p">(</span><span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

783

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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

784

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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python">                    <span class="n" style="color: #333;">new_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_lineage</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

785

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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python">                            <span class="n" style="color: #333;">lineage_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"lineage_id"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python">                            <span class="n" style="color: #333;">parent_lineage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_lineage</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

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<pre style="margin: 0;">+<span id="LC787" class="line" lang="python">                            <span class="n" style="color: #333;">origin_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

788

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<pre style="margin: 0;">+<span id="LC788" class="line" lang="python">                            <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

789

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<pre style="margin: 0;">+<span id="LC789" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_collection</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

790

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<pre style="margin: 0;">+<span id="LC790" class="line" lang="python">                    <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new_lineage</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

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<pre style="margin: 0;">+<span id="LC791" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

792

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<pre style="margin: 0;">+<span id="LC792" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Completion of speciation</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

793

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<pre style="margin: 0;">+<span id="LC793" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

794

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<pre style="margin: 0;">+<span id="LC794" class="line" lang="python">                    <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

795

</td>

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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python">                    <span class="n" style="color: #333;">lineage</span><span class="p">.</span><span class="n" style="color: #333;">speciation_completion_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

796

</td>

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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"species_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

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<pre style="margin: 0;">+<span id="LC797" class="line" lang="python">                    <span class="n" style="color: #333;">lineage</span><span class="p">.</span><span class="n" style="color: #333;">species_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage_data</span><span class="p">[</span><span class="n" style="color: #333;">phase_idx</span><span class="p">][</span><span class="s" style="color: #d14;">"species_id"</span><span class="p">]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

798

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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python">                    <span class="n" style="color: #333;">orthospecies_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lineage</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

799

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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

800

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<pre style="margin: 0;">+<span id="LC800" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">event_type_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

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<pre style="margin: 0;">+<span id="LC801" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Extinction of an incipient_species lineage</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

802

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<pre style="margin: 0;">+<span id="LC802" class="line" lang="python">                    <span class="n" style="color: #333;">lineage_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rng</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

803

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python">                    <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">].</span><span class="n" style="color: #333;">extinction_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_time</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

804

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">incipient_species_lineages</span><span class="p">[</span><span class="n" style="color: #333;">lineage_idx</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

805

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

806

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Unexpected event type index: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">event_type_idx</span><span class="p">))</span></span>

</pre>

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800

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<td class="new_line diff-line-num" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

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<pre style="margin: 0;"> <span id="LC807" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

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<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

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<pre style="margin: 0;"> <span id="LC808" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_new_lineage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

802

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<td class="new_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python">            <span class="n" style="color: #333;">lineage_id</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="2b98aed557dd248628ac8cf42ec071f41934db26">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#2b98aed557dd248628ac8cf42ec071f41934db26"><strong>tests/data/trees/pythonidae.lower.mle.nex</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#NEXUS</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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3

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

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

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    DIMENSIONS NTAX=33;</span>

</pre>

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6

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

</pre>

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7

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

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">        python_sebae</span>

</pre>

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9

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

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">        python_curtus</span>

</pre>

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11

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

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">        morelia_spilota</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">        morelia_clastolepis</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">        morelia_kinghorni</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">        morelia_nauta</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">        morelia_oenpelliensis</span>

</pre>

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19

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

</pre>

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20

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

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">        antaresia_stimsoni</span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">        antaresia_childreni</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">        morelia_carinata</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">        morelia_viridisn</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">        morelia_viridiss</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">        apodora_papuana</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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

</pre>

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

</pre>

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29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">        liasis_mackloti</span>

</pre>

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30

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

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">        antaresia_ramsayi</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">        liasis_albertisii</span>

</pre>

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33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">        bothrochilus_boa</span>

</pre>

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34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">        morelia_boeleni</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">        python_timoriensis</span>

</pre>

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36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">        python_reticulatus</span>

</pre>

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37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">        xenopeltis_unicolor</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">        candoia_aspera</span>

</pre>

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39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">        loxocemus_bicolor</span>

</pre>

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40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">  ;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">END;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">BEGIN TREES;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">    TREE 0 = [&U] (((python_regius:0.1058922755,((python_sebae:0.0629755585,python_molurus:0.0335903967):0.02165,python_curtus:0.1067094932):0.016163):0.032743,(((((morelia_bredli:0.0274921037,morelia_spilota:0.0241663426):0.026356,((morelia_tracyae:0.0377936102,((morelia_clastolepis:0.0045446653,(morelia_kinghorni:0.0075825724,morelia_nauta:0.0086155842):0.004182):0.018597,morelia_amethistina:0.0227641045):0.007181):0.024796,morelia_oenpelliensis:0.0579745143):0.004283):0.031732,((antaresia_maculosa:0.0679212061,(antaresia_perthensis:0.0760812159,(antaresia_stimsoni:0.0152390165,antaresia_childreni:0.023141749):0.032397):0.012848):0.011617,(morelia_carinata:0.0660356718,(morelia_viridisn:0.0377499268,morelia_viridiss:0.0473589755):0.027329):0.013482):0.015469):0.006602,(((((apodora_papuana:0.0670782319,liasis_olivaceus:0.0430801028):0.010168,(liasis_fuscus:0.0194903208,liasis_mackloti:0.0141916418):0.048505):0.013422,(antaresia_melanocephalus:0.0380695554,antaresia_ramsayi:0.0325474267):0.043626):0.007734,(liasis_albertisii:0.0542142498,bothrochilus_boa:0.0638595214):0.038444):0.002713,morelia_boeleni:0.0843874314):0.002859):0.027099,(python_timoriensis:0.074479767,python_reticulatus:0.0562613055):0.06004):0.030952):0.060789,(xenopeltis_unicolor:0.1983677797,candoia_aspera:0.4092923305):0.048508,loxocemus_bicolor:0.2627888765);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">END;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="f07a50deefbad92586a94e92793c506a2350c0b8">

<a href="https://salsa.debian.org/med-team/python-dendropy/-/compare/409cf8ee2abbffeef727202538545d994f8e1cf2...6f1153b5e08ccd29b29f4cebd4cb7161e25c5c81#f07a50deefbad92586a94e92793c506a2350c0b8"><strong>tests/data/trees/pythonidae.upper.mle.nex</strong></a>

<hr>

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1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#NEXUS</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    DIMENSIONS NTAX=33;</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">        PYTHON_SEBAE</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">        PYTHON_CURTUS</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">        MORELIA_SPILOTA</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">        MORELIA_CLASTOLEPIS</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">        MORELIA_KINGHORNI</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">        MORELIA_NAUTA</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">        MORELIA_OENPELLIENSIS</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

</td>

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">        ANTARESIA_STIMSONI</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

</td>

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">        ANTARESIA_CHILDRENI</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">        MORELIA_CARINATA</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">        MORELIA_VIRIDISN</span>

</pre>

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</tr>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">        MORELIA_VIRIDISS</span>

</pre>

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</tr>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">        APODORA_PAPUANA</span>

</pre>

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</tr>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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

</pre>

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</tr>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">        LIASIS_MACKLOTI</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">        ANTARESIA_RAMSAYI</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">        LIASIS_ALBERTISII</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

</td>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">        BOTHROCHILUS_BOA</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

</td>

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

<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">        MORELIA_BOELENI</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

</td>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">        PYTHON_TIMORIENSIS</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

</td>

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">        PYTHON_RETICULATUS</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

</td>

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

<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">        XENOPELTIS_UNICOLOR</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

</td>

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

<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">        CANDOIA_ASPERA</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

</td>

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

<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">        LOXOCEMUS_BICOLOR</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

</td>

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">  ;</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">END;</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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

<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">BEGIN TREES;</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">    TREE 0 = [&U] (((PYTHON_REGIUS:0.1058922755,((PYTHON_SEBAE:0.0629755585,PYTHON_MOLURUS:0.0335903967):0.02165,PYTHON_CURTUS:0.1067094932):0.016163):0.032743,(((((MORELIA_BREDLI:0.0274921037,MORELIA_SPILOTA:0.0241663426):0.026356,((MORELIA_TRACYAE:0.0377936102,((MORELIA_CLASTOLEPIS:0.0045446653,(MORELIA_KINGHORNI:0.0075825724,MORELIA_NAUTA:0.0086155842):0.004182):0.018597,MORELIA_AMETHISTINA:0.0227641045):0.007181):0.024796,MORELIA_OENPELLIENSIS:0.0579745143):0.004283):0.031732,((ANTARESIA_MACULOSA:0.0679212061,(ANTARESIA_PERTHENSIS:0.0760812159,(ANTARESIA_STIMSONI:0.0152390165,ANTARESIA_CHILDRENI:0.023141749):0.032397):0.012848):0.011617,(MORELIA_CARINATA:0.0660356718,(MORELIA_VIRIDISN:0.0377499268,MORELIA_VIRIDISS:0.0473589755):0.027329):0.013482):0.015469):0.006602,(((((APODORA_PAPUANA:0.0670782319,LIASIS_OLIVACEUS:0.0430801028):0.010168,(LIASIS_FUSCUS:0.0194903208,LIASIS_MACKLOTI:0.0141916418):0.048505):0.013422,(ANTARESIA_MELANOCEPHALUS:0.0380695554,ANTARESIA_RAMSAYI:0.0325474267):0.043626):0.007734,(LIASIS_ALBERTISII:0.0542142498,BOTHROCHILUS_BOA:0.0638595214):0.038444):0.002713,MORELIA_BOELENI:0.0843874314):0.002859):0.027099,(PYTHON_TIMORIENSIS:0.074479767,PYTHON_RETICULATUS:0.0562613055):0.06004):0.030952):0.060789,(XENOPELTIS_UNICOLOR:0.1983677797,CANDOIA_ASPERA:0.4092923305):0.048508,LOXOCEMUS_BICOLOR:0.2627888765);</span>

</pre>

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45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">END;</span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span></pre>

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