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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/augur">Debian Med / augur</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117">68d6dee1</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-25T14:44:04+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.0.3</pre>
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<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">
augur/__version__.py
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<a href="#fec638407816347df368936c41e5929f42fd4fe6">
augur/data/schema-export-v2.json
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<li class="file-stats">
<a href="#104ddc27c2db78b040d33b5412a2de3d66f15177">
augur/refine.py
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<a href="#a0dd53664ee83560f1b40e93ea9bccd88fa56713">
augur/validate_export.py
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tests/functional/refine.t
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tests/functional/refine/aligned.fasta
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tests/functional/refine/integer_branch_lengths.json
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tests/functional/refine/metadata.tsv
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tests/functional/refine/mutations_per_site_branch_lengths.json
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tests/functional/refine/not_time_tree.nwk
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tests/functional/refine/tree.nwk
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tests/functional/refine/tree_raw.nwk
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tests/test_validate_export.py
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</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">@@ -3,6 +3,16 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## __NEXT__</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.0.3 (23 October 2020)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> refine: Report divergence by number of mutations as an integer instead of a floating point value <span class="p">[</span><span class="nv" style="color: #008080;">#618</span><span class="p">][]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> validate: Allow internal nodes with a single child and do not allow duplicate node names <span class="p">[</span><span class="nv" style="color: #008080;">#621</span><span class="p">][]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#618</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/618</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#621</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/621</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.0.2 (8 September 2020)</span></span>
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<li id="a1a05fb3eb681edc11e8c987f65967f416af0ee1">
<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" 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;">'10.0.<span class="idiff left right">2</span>'</span></span>
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<td class="diff-line-num new new_line" 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="LC1" 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;">'10.0.<span class="idiff left right">3</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_augur_version_compatible</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#fec638407816347df368936c41e5929f42fd4fe6"><strong>augur/data/schema-export-v2.json</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">@@ -445,9 +445,9 @@</td>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"children"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Child nodes. Recursive structure. Terminal nodes do not have this property."</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$comment"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Polytomies (more than 2 items) allowed."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$comment"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Polytomies (more than 2 items) allowed<span class="idiff left right">, as are nodes with a single child</span>."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"array"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"minItems"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"minItems"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"items"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="nl">"$ref"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#/properties/tree"</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#104ddc27c2db78b040d33b5412a2de3d66f15177"><strong>augur/refine.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">@@ -6,7 +6,7 @@ import os, shutil, time, sys</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Phylo</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">read_tree</span><span class="p">,</span> <span class="n" style="color: #333;">get_numerical_dates</span><span class="p">,</span> <span class="n" style="color: #333;">write_json</span><span class="p">,</span> <span class="n" style="color: #333;">InvalidTreeError</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime.vcf_utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_vcf</span><span class="p">,</span> <span class="n" style="color: #333;">write_vcf</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime.seq_utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">profile_maps</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">dates</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">branch_length_inference</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">confidence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">resolve_polytomies</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">max_iter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">precision</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -145,10 +145,15 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC147" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fake alignment to appease treetime when only using it for naming nodes...</span></span>
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149
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">timetree</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: alignment is required for ancestral reconstruction or timetree inference"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: alignment is required for ancestral reconstruction or timetree inference"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stderr</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">divergence_units</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'mutations'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: alignment is required for divergence in units of mutations"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fake alignment to appease treetime when only using it for naming nodes...</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">,</span> <span class="n" style="color: #333;">Seq</span><span class="p">,</span> <span class="n" style="color: #333;">Align</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">():</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,7 +161,7 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Align</span><span class="p">.</span><span class="n" style="color: #333;">MultipleSeqAlignment</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">)</span></span>
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157
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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">().</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'.vcf'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.vcf.gz'</span><span class="p">]]):</span></span>
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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
158
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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
163
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<pre style="margin: 0;"> <span id="LC163" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">vcf_reference</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: a reference Fasta is required with VCF-format alignments"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: a reference Fasta is required with VCF-format alignments"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stderr</span></span><span class="p">)</span></span>
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160
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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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161
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<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
162
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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">compress_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_vcf</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">vcf_reference</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(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="190" style="width: 35px; color: rgba(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">@@ -185,7 +190,7 @@ def run(args):</td>
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185
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<td class="diff-line-num new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">timetree</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
186
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<td class="diff-line-num new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># load meta data and covert dates to numeric</span></span>
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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
187
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<td class="diff-line-num new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: meta data with dates is required for time tree reconstruction"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: meta data with dates is required for time tree reconstruction"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stderr</span></span><span class="p">)</span></span>
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189
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
190
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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_metadata</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">)</span></span>
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191
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">year_bounds</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" style="width: 35px; color: rgba(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="222" style="width: 35px; color: rgba(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">@@ -217,7 +222,7 @@ def run(args):</td>
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217
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'skyline'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">skyline</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">],</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">conf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span></span>
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218
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<td class="diff-line-num new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">skyline</span><span class="p">.</span><span class="n" style="color: #333;">y</span><span class="p">],</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">conf</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]]</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: skyline optimization by TreeTime has failed."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: skyline optimization by TreeTime has failed."</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stderr</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">attributes</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">'numdate'</span><span class="p">,</span> <span class="s" style="color: #d14;">'clock_length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mutation_length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'raw_date'</span><span class="p">,</span> <span class="s" style="color: #d14;">'date'</span><span class="p">])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -241,13 +246,35 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">divergence_units</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'mutations-per-site'</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#default</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">divergence_units</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'mutations'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tt</span><span class="p">.</span><span class="n" style="color: #333;">seq_len</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'nodes'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC249" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">timetree</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">tt</span><span class="p">.</span><span class="n" style="color: #333;">infer_ancestral_sequences</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">nuc_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">profile_maps</span><span class="p">[</span><span class="s" style="color: #d14;">'nuc'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">are_sequence_states_different</span><span class="p">(</span><span class="n" style="color: #333;">nuc1</span><span class="p">,</span> <span class="n" style="color: #333;">nuc2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"><span class="s" style="color: #d14;"> determine whether two ancestral states should count as mutation for divergence estimates</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"><span class="s" style="color: #d14;"> while correctly accounting for ambiguous nucleotides</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nuc1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">nuc2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N'</span><span class="p">]:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nuc_map</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nuc2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nuc_map</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">nuc_map</span><span class="p">[</span><span class="n" style="color: #333;">nuc1</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nuc_map</span><span class="p">[</span><span class="n" style="color: #333;">nuc2</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">find_clades</span><span class="p">():</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">n_muts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">([</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">position</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ancestral</span><span class="p">,</span> <span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">derived</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">mutations</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">are_sequence_states_different</span><span class="p">(</span><span class="n" style="color: #333;">ancestral</span><span class="p">,</span> <span class="n" style="color: #333;">derived</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="p">])</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"></span>
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246
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<td class="diff-line-num new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">timetree</span><span class="p">:</span></span>
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247
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<td class="diff-line-num new_line old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'nodes'</span><span class="p">][</span><span class="n" style="color: #333;">node</span><span class="p">][</span><span class="s" style="color: #d14;">'mutation_length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">L</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'nodes'</span><span class="p">][</span><span class="n" style="color: #333;">node</span><span class="p">][</span><span class="s" style="color: #d14;">'branch_length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">L</span></span>
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<td class="diff-line-num new old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'nodes'</span><span class="p">][</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'mutation_length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_muts</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'nodes'</span><span class="p">][</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'branch_length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_muts</span></span>
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249
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: divergence unit"</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">divergence_units</span><span class="p">,</span><span class="s" style="color: #d14;">"not supported!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: divergence unit"</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">divergence_units</span><span class="p">,</span><span class="s" style="color: #d14;">"not supported!"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stderr</span></span><span class="p">)</span></span>
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251
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"></span>
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Export refined tree and node data</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#a0dd53664ee83560f1b40e93ea9bccd88fa56713"><strong>augur/validate_export.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">@@ -7,6 +7,20 @@ and refactored over time.</td>
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<pre style="margin: 0;"> <span id="LC7" 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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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ensure_no_duplicate_names</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">ValidateError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;"> Check that all node names are identical, which is required for auspice (v2) JSONs.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">names</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="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">recurse</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidateError</span><span class="p">(</span><span class="s" style="color: #d14;">f"Node </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">node</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> appears multiple times in the tree."</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">names</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"children"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">recurse</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="p">[</span><span class="s" style="color: #d14;">"children"</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">recurse</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">collectTreeAttrsV2</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">warn</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> Collect all keys specified on `node["node_attrs"]` throughout the tree</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">@@ -82,6 +96,8 @@ def verifyMainJSONIsInternallyConsistent(data, ValidateError):</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating that the JSON is internally consistent..."</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">ensure_no_duplicate_names</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"tree"</span><span class="p">],</span> <span class="n" style="color: #333;">ValidateError</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"entropy"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"meta"</span><span class="p">][</span><span class="s" style="color: #d14;">"panels"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"genome_annotations"</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;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"meta"</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"The entropy panel has been specified but annotations don't exist."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#9753651334e00be71d51aba2fccf83cd1d0508c5"><strong>tests/functional/refine.t</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="nv" style="color: #008080;">Integration</span> <span class="nv" style="color: #008080;">tests</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">augur</span> <span class="nv" style="color: #008080;">refine</span><span class="o" style="font-weight: 600;">.</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">pushd</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="p">"</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">export</span> <span class="nv" style="color: #008080;">AUGUR</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">../../bin/augur</span><span class="p">"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="nv" style="color: #008080;">Try</span> <span class="nv" style="color: #008080;">building</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="o" style="font-weight: 600;">.</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nv" style="color: #008080;">AUGUR</span><span class="p">}</span> <span class="nv" style="color: #008080;">refine</span> <span class="o" style="font-weight: 600;">\</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree_raw.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">alignment</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/aligned.fasta</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">metadata</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/metadata.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">timetree</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">coalescent</span> <span class="nv" style="color: #008080;">opt</span> <span class="o" style="font-weight: 600;">\</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">confidence</span> <span class="o" style="font-weight: 600;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">inference</span> <span class="nv" style="color: #008080;">marginal</span> <span class="o" style="font-weight: 600;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"> <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">TreeTime</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">python3</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="s2" style="color: #d14;">/../../scripts/diff_trees.py</span><span class="p">"</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree.nwk</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">significant</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">digits</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"> <span class="p">{}</span></span>
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<td class="diff-line-num new new_line" 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="perl"></span>
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<td class="diff-line-num new new_line" 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="perl"><span class="nv" style="color: #008080;">Build</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">mutations</span> <span class="nv" style="color: #008080;">as</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">reported</span> <span class="nv" style="color: #008080;">divergence</span> <span class="nv" style="color: #008080;">unit</span><span class="o" style="font-weight: 600;">.</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nv" style="color: #008080;">AUGUR</span><span class="p">}</span> <span class="nv" style="color: #008080;">refine</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree_raw.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">alignment</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/aligned.fasta</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">metadata</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/metadata.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">timetree</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">coalescent</span> <span class="nv" style="color: #008080;">opt</span> <span class="o" style="font-weight: 600;">\</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">confidence</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">inference</span> <span class="nv" style="color: #008080;">marginal</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"> <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"> <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">TreeTime</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">python3</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="s2" style="color: #d14;">/../../scripts/diff_trees.py</span><span class="p">"</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree.nwk</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">significant</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">digits</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"><span class="nv" style="color: #008080;">Run</span> <span class="nv" style="color: #008080;">refine</span> <span class="nv" style="color: #008080;">without</span> <span class="nv" style="color: #008080;">inferring</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"><span class="nv" style="color: #008080;">This</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">one</span> <span class="nv" style="color: #008080;">way</span> <span class="nv" style="color: #008080;">to</span> <span class="nv" style="color: #008080;">get</span> <span class="nv" style="color: #008080;">named</span> <span class="nv" style="color: #008080;">internal</span> <span class="nv" style="color: #008080;">nodes</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">downstream</span> <span class="nv" style="color: #008080;">analyses</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">does</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">require</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">alignment</span> <span class="nv" style="color: #008080;">FASTA</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nv" style="color: #008080;">AUGUR</span><span class="p">}</span> <span class="nv" style="color: #008080;">refine</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree_raw.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">metadata</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/metadata.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">coalescent</span> <span class="nv" style="color: #008080;">opt</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">confidence</span> <span class="o" style="font-weight: 600;">\</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">inference</span> <span class="nv" style="color: #008080;">marginal</span> <span class="o" style="font-weight: 600;">\</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">per</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">site</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"> <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"> <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="p">,</span> <span class="nv" style="color: #008080;">given</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">should</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">be</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="o" style="font-weight: 600;">.</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">python3</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="s2" style="color: #d14;">/../../scripts/diff_trees.py</span><span class="p">"</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/not_time_tree.nwk</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">significant</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">digits</span> <span class="mi" style="color: #099;">2</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"> <span class="p">{}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">python3</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="s2" style="color: #d14;">/../../scripts/diff_jsons.py</span><span class="p">"</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/mutations_per_site_branch_lengths.json</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">significant</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">digits</span> <span class="mi" style="color: #099;">0</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"> <span class="p">{}</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="perl"><span class="nv" style="color: #008080;">Run</span> <span class="nv" style="color: #008080;">refine</span> <span class="nv" style="color: #008080;">again</span> <span class="nv" style="color: #008080;">without</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="p">,</span> <span class="nv" style="color: #008080;">but</span> <span class="nv" style="color: #008080;">request</span> <span class="nv" style="color: #008080;">number</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">mutations</span> <span class="nv" style="color: #008080;">per</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">as</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">divergence</span> <span class="nv" style="color: #008080;">unit</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl"><span class="nv" style="color: #008080;">This</span> <span class="nv" style="color: #008080;">approach</span> <span class="nv" style="color: #008080;">only</span> <span class="nv" style="color: #008080;">works</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">we</span> <span class="nv" style="color: #008080;">provide</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">alignment</span> <span class="nv" style="color: #008080;">FASTA</span><span class="o" style="font-weight: 600;">.</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nv" style="color: #008080;">AUGUR</span><span class="p">}</span> <span class="nv" style="color: #008080;">refine</span> <span class="o" style="font-weight: 600;">\</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree_raw.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">alignment</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/aligned.fasta</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">metadata</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/metadata.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">coalescent</span> <span class="nv" style="color: #008080;">opt</span> <span class="o" style="font-weight: 600;">\</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">confidence</span> <span class="o" style="font-weight: 600;">\</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">inference</span> <span class="nv" style="color: #008080;">marginal</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"> <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="perl"> <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="p">,</span> <span class="nv" style="color: #008080;">given</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">should</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">be</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">python3</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="s2" style="color: #d14;">/../../scripts/diff_trees.py</span><span class="p">"</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/not_time_tree.nwk</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">significant</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">digits</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="perl"> <span class="p">{}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">python3</span> <span class="p">"</span><span class="si" style="color: #d14;">$TESTDIR</span><span class="s2" style="color: #d14;">/../../scripts/diff_jsons.py</span><span class="p">"</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/integer_branch_lengths.json</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">significant</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">digits</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="perl"> <span class="p">{}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="perl"><span class="nv" style="color: #008080;">Run</span> <span class="nv" style="color: #008080;">refine</span> <span class="nv" style="color: #008080;">again</span> <span class="nv" style="color: #008080;">without</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="p">,</span> <span class="nv" style="color: #008080;">but</span> <span class="nv" style="color: #008080;">try</span> <span class="nv" style="color: #008080;">to</span> <span class="nv" style="color: #008080;">request</span> <span class="nv" style="color: #008080;">number</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">mutations</span> <span class="nv" style="color: #008080;">per</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">as</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">divergence</span> <span class="nv" style="color: #008080;">unit</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="perl"><span class="nv" style="color: #008080;">This</span> <span class="nv" style="color: #008080;">approach</span> <span class="nv" style="color: #008080;">does</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">make</span> <span class="nv" style="color: #008080;">sense</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">should</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">work</span> <span class="nv" style="color: #008080;">without</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">alignment</span> <span class="nv" style="color: #008080;">FASTA</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nv" style="color: #008080;">AUGUR</span><span class="p">}</span> <span class="nv" style="color: #008080;">refine</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/tree_raw.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">metadata</span> <span class="p">"</span><span class="s2" style="color: #d14;">refine/metadata.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tree</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/tree.nwk</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/branch_lengths.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">coalescent</span> <span class="nv" style="color: #008080;">opt</span> <span class="o" style="font-weight: 600;">\</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">confidence</span> <span class="o" style="font-weight: 600;">\</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">inference</span> <span class="nv" style="color: #008080;">marginal</span> <span class="o" style="font-weight: 600;">\</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"> <span class="o" style="font-weight: 600;">*</span><span class="nv" style="color: #008080;">ERROR:</span> <span class="nv" style="color: #008080;">alignment</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">required</span><span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="perl"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">popd</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span></pre>
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<li id="3402cd16e2e0ca24b264d77ca9505613a8aff4a4">
<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#3402cd16e2e0ca24b264d77ca9505613a8aff4a4"><strong>tests/functional/refine/aligned.fasta</strong></a>
The diff for this file was not included because it is too large.
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<li id="15ad9a810847925c2363dcf3d9e595d9886e9350">
<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#15ad9a810847925c2363dcf3d9e595d9886e9350"><strong>tests/functional/refine/integer_branch_lengths.json</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"alignment"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"refine/aligned.fasta"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"generated_by"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"program"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"augur"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"10.0.2"</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"input_tree"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"refine/tree_raw.nwk"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"nodes"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"BRA/2016/FC_6706"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">12</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"COL/FLR_00008/2015"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">5</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Colombia/2016/ZC204Se"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">5</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"DOM/2016/BB_0183"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">24</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"EcEs062_16"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">18</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"HND/2016/HU_ME59"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">13</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"KX369547.1"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">3</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000000"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">0</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000001"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">7</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000002"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">2</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000003"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">0</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000004"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">1</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000005"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">2</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000006"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">11</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000007"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">2</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000008"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">6</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"PAN/CDC_259359_V1_V3/2015"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">9</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"PRVABC59"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">22</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"VEN/UF_1/2016"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">7</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"ZKC2/2016"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">28</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="json"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">strain virus accession date region country division city db segment authors url title journal paper_url</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">PAN/CDC_259359_V1_V3/2015 zika KX156774 2015-12-18 North America Panama Panama Panama genbank genome Shabman et al https://www.ncbi.nlm.nih.gov/nuccore/KX156774 Direct Submission Submitted (29-APR-2016) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">COL/FLR_00024/2015 zika MF574569 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574569 Direct Submission Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">PRVABC59 zika KU501215 2015-12-XX North America Puerto Rico Puerto Rico Puerto Rico genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501215 Phylogeny of Zika Virus in Western Hemisphere, 2015 Emerging Infect. Dis. 22 (5), 933-935 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27088323</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">COL/FLR_00008/2015 zika MF574562 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574562 Direct Submission Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Colombia/2016/ZC204Se zika KY317939 2016-01-06 South America Colombia Colombia Colombia genbank genome Quick et al https://www.ncbi.nlm.nih.gov/nuccore/KY317939 Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Nat Protoc 12 (6), 1261-1276 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538739</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ZKC2/2016 zika KX253996 2016-02-16 Oceania American Samoa American Samoa American Samoa genbank genome Wu et al https://www.ncbi.nlm.nih.gov/nuccore/KX253996 Direct Submission Submitted (18-MAY-2016) Center for Diseases Control and Prevention of Guangdong Province; National Institute of Viral Disease Control and Prevention, China https://www.ncbi.nlm.nih.gov/pubmed/</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">VEN/UF_1/2016 zika KX702400 2016-03-25 South America Venezuela Venezuela Venezuela genbank genome Blohm et al https://www.ncbi.nlm.nih.gov/nuccore/KX702400 Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant Genome Announc 5 (17), e00231-17 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28450510</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">DOM/2016/BB_0059 zika KY785425 2016-04-04 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785425 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">BRA/2016/FC_6706 zika KY785433 2016-04-08 South America Brazil Brazil Brazil genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785433 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">DOM/2016/BB_0183 zika KY785420 2016-04-18 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785420 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">EcEs062_16 zika KX879603 2016-04-XX South America Ecuador Ecuador Ecuador genbank genome Marquez et al https://www.ncbi.nlm.nih.gov/nuccore/KX879603 First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador Genome Announc 5 (8), e01673-16 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28232448</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">HND/2016/HU_ME59 zika KY785418 2016-05-13 North America Honduras Honduras Honduras genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785418 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#926067ba4da7b3682f291a190594bc39af45f6b6"><strong>tests/functional/refine/mutations_per_site_branch_lengths.json</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"alignment"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">null</span><span class="p">,</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"generated_by"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"program"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"augur"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" 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
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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="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"10.0.2"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"input_tree"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"refine/tree_raw.nwk"</span><span class="p">,</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"nodes"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"BRA/2016/FC_6706"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00119745</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"COL/FLR_00008/2015"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00046961</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Colombia/2016/ZC204Se"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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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="LC16" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00047184</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"DOM/2016/BB_0183"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00226698</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"EcEs062_16"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00167718</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"HND/2016/HU_ME59"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00125764</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"KX369547.1"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00027828</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000000"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.001</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000001"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.000651</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000002"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.000184</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000003"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">2e-06</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000004"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">9.3e-05</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000005"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.000209</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000006"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.000949</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000007"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.000192</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"NODE_0000008"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.000579</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"PAN/CDC_259359_V1_V3/2015"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00083922</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"PRVABC59"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00206996</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"VEN/UF_1/2016"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00067495</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"ZKC2/2016"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch_length"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mf" style="color: #099;">0.00260941</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="json"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#e44a03e78ece9718b6585c861a52f11770203b56"><strong>tests/functional/refine/not_time_tree.nwk</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">(KX369547.1:0.00027828,ZKC2/2016:0.00260941,((EcEs062_16:0.00167718,DOM/2016/BB_0183:0.00226698)NODE_0000002:0.00018400,((HND/2016/HU_ME59:0.00125764,PRVABC59:0.00206996)NODE_0000004:0.00009300,(BRA/2016/FC_6706:0.00119745,(Colombia/2016/ZC204Se:0.00047184,(PAN/CDC_259359_V1_V3/2015:0.00083922,(COL/FLR_00008/2015:0.00046961,VEN/UF_1/2016:0.00067495)NODE_0000008:0.00057900)NODE_0000007:0.00019200)NODE_0000006:0.00094900)NODE_0000005:0.00020900)NODE_0000003:0.00000200)NODE_0000001:0.00065100)NODE_0000000:0.00100000;</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#2271ac9ef26d30e1ca6e9944ba514a53b573d3b5"><strong>tests/functional/refine/tree.nwk</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">((Colombia/2016/ZC204Se:0.00105368,(PAN/CDC_259359_V1_V3/2015:0.00076051,(COL/FLR_00008/2015:0.00044440,VEN/UF_1/2016:0.00089377)NODE_0000008:0.00038502)NODE_0000007:0.00019253)NODE_0000001:0.00080159,(BRA/2016/FC_6706:0.00214920,(ZKC2/2016:0.00173693,(HND/2016/HU_ME59:0.00206150,PRVABC59:0.00135309)NODE_0000004:0.00013537,(EcEs062_16:0.00175918,DOM/2016/BB_0183:0.00184905)NODE_0000002:0.00021565)NODE_0000003:0.00013737)NODE_0000005:0.00019772)NODE_0000006:0.00100000;</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#354977f95cf1705ce128dfa168c8ea64e078f857"><strong>tests/functional/refine/tree_raw.nwk</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">(KX369547.1:0.00027828,(((BRA/2016/FC_6706:0.00119745,((PAN/CDC_259359_V1_V3/2015:0.00083922,(COL/FLR_00008/2015:0.00046961,VEN/UF_1/2016:0.00067495):0.00057900):0.00019200,Colombia/2016/ZC204Se:0.00047184):0.00094900):0.00020900,(HND/2016/HU_ME59:0.00125764,PRVABC59:0.00206996):0.00009300):0.00000200,(EcEs062_16:0.00167718,DOM/2016/BB_0183:0.00226698):0.00018400):0.00065100,ZKC2/2016:0.00260941):0.00000000;</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/68d6dee105679cee78446c2a26a1930c0dd2b117#1413df03b1691f47d656533e8f1148c41d67a251"><strong>tests/test_validate_export.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Bio.Phylo</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC5" 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="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># we assume (and assert) that this script is running from the tests/ directory</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">).</span><span class="n" style="color: #333;">parent</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">augur.export_v2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">convert_tree_to_json_structure</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">augur.validate</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ValidateError</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">augur.validate_export</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ensure_no_duplicate_names</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestValidateExport</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_export_without_duplicate_names</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="LC17" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create a tree with unique tip names.</span></span>
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<pre style="margin: 0;">+<span id="LC18" 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;">Bio</span><span class="p">.</span><span class="n" style="color: #333;">Phylo</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="s" style="color: #d14;">"root(A, internal(B, C))"</span><span class="p">),</span> <span class="s" style="color: #d14;">"newick"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"B"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"C"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"root"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"internal"</span><span class="p">:</span> <span class="p">{}}</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">convert_tree_to_json_structure</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">ensure_no_duplicate_names</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">ValidateError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_export_with_duplicate_names</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="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create a tree with duplicate tip names.</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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;">Bio</span><span class="p">.</span><span class="n" style="color: #333;">Phylo</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="s" style="color: #d14;">"root(A, internal(B, B))"</span><span class="p">),</span> <span class="s" style="color: #d14;">"newick"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"B"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"root"</span><span class="p">:</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"internal"</span><span class="p">:</span> <span class="p">{}}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">convert_tree_to_json_structure</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">ValidateError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">ensure_no_duplicate_names</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">ValidateError</span><span class="p">)</span></span></pre>
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