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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-ete3">Debian Med / python-ete3</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ete3/-/commit/b8ac6d018f1f128acb48ec4b4005cfe231412100">b8ac6d01</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T17:51:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">move python3-numpy to Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ete3/-/commit/961e7a0fa5330fd14b29985bbf4babe31c1065c6">961e7a0f</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T18:58:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">restore ete3/tools
These components are needed for superficial autodep8 autopkgtest
to go through; chances are the package does not work without it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ete3/-/commit/0c53f2edaad49d3c5962bdd952b6bd9ba53c54a5">0c53f2ed</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T19:08:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pmodeltest_executable.patch to address lintian warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ete3/-/commit/c0c1d050ffdaed8b08c60111b05be21bed9c41d0">c0c1d050</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T19:20:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add repository informations to upstream/metadata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ete3/-/commit/7e29f172e030540ff2bdc33008ff299de74f7789">7e29f172</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T19:21:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ete3/-/commit/f25a591c238f4e9c6fb3cba5de339a3653ec2a5a">f25a591c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T19:22:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#333361735e9113aca63b92115c03317a5b8bae73">
<span class="new-file">
+
debian/patches/pmodeltest_executable.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#570771a5dc304b73613bd7c2aa4a71358ae984dc">
debian/python3-ete3.pyremove
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-ete3 (3.1.2+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Moved python3-numpy from Recommends to Depends. (Closes: #972983)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Restored ete3/tools:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - it allowed autodep8 autopkgtest to succeed,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> - pmodeltest_executable.patch wrapped up to address the reintroduced</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="plaintext"> executable not ELF nor script.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Added repository information to upstream/metadata.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Submit.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 04 Nov 2020 19:21:18 +0100</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">python-ete3 (3.1.2+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -29,9 +29,9 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> python3-six</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Recommends: ${python3:Recommends}</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> python3-lxml,</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> python3-qt-binding,</span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> python3-pyqt5.qtopengl,</span>
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<li id="333361735e9113aca63b92115c03317a5b8bae73">
<a href="https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a#333361735e9113aca63b92115c03317a5b8bae73"><strong>debian/patches/pmodeltest_executable.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: make pmodeltest.py a genuine python3 executable</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This issue has been caught by lintian, as an executable not ELF nor script.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-11-04</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-ete3.orig/ete3/tools/ete_build_lib/apps.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-ete3/ete3/tools/ete_build_lib/apps.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -72,7 +72,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> 'iqtree' : "%BIN%/iqtree -nt %CORES%",</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 'raxml-pthreads' : "%BIN%/raxmlHPC-PTHREADS-SSE3 -T%CORES%",</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 'raxml' : "%BIN%/raxmlHPC-SSE3",</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'pmodeltest' : "python %BIN%/pmodeltest.py --nprocs %CORES% --phyml %BIN%/phyml",</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'pmodeltest' : "%BIN%/pmodeltest.py --nprocs %CORES% --phyml %BIN%/phyml",</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> 'dialigntx' : "%BIN%/dialign-tx %BIN%/dialigntx_conf",</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> 'fasttree' : "export OMP_NUM_THREADS=%CORES%; %BIN%/FastTree",</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> 'statal' : "%BIN%/statal",</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-ete3.orig/ete3/tools/ete_build_lib/task/pmodeltest.py</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-ete3/ete3/tools/ete_build_lib/task/pmodeltest.py</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -1,3 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#! /usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> from __future__ import absolute_import</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> import re</span></pre>
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<a href="https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">syntax_fixes.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">pmodeltest_executable.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a#570771a5dc304b73613bd7c2aa4a71358ae984dc"><strong>debian/python3-ete3.pyremove</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">test.*</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">ete3/test/*</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">ete3/tools/*</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">ete3/ncbi_taxonomy/SQLite-Levenshtein/*</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">examples/*</span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">examples/*</span></pre>
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<a href="https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Submit: https://github.com/etetoolkit/ete/issues/new</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> - Author: Jaime Huerta-Cepas and François Serra and Peer Bork</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Title: ></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">@@ -8,3 +9,6 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> URL: https://academic.oup.com/mbe/article/33/6/1635/2579822</span>
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9
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> eprint: ></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> https://academic.oup.com/mbe/article-pdf/33/6/1635/7953632/msw046.pdf</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Repository: https://github.com/etetoolkit/ete.git</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Repository-Browse: https://github.com/etetoolkit/ete</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Bug-Database: https://github.com/etetoolkit/ete/issues</span></pre>
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