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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/phyx">Debian Med / phyx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/8ab2c63e12c6ef699adf6a7bfbcf994c3bf71029">8ab2c63e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T19:21:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add changelog entry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/54631f6a5b04e0f4abccf13fff202e14bc652dde">54631f6a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T19:21:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/aae7183c63687b9e84a2eab133892a689c9fe98f">aae7183c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T19:21:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/18d4d89037074256b3bc3c6ec8a5c6ec939b614f">18d4d890</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T19:49:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">phyx (0.999+ds-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add new d/u/metadata file</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></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"> [ Afif Elghraoui ]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Remove myself from Uploaders</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> [ Shayan Doust ]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Port couple of python files from python2 to python3</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Closes: #937285</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Set debhelper 12 from 11</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></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">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> -- Shayan Doust <hello@shayandoust.me> Wed, 11 Sep 2019 21:17:58 +0200</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">phyx (0.999+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<a href="https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f#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">@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> liblapack-dev,</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libnlopt-cxx-dev,</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libnlopt-dev,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libatlas-cpp-0.6-dev,</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libarmadillo-dev</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/phyx</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/phyx.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/FePhyFoFum/phyx</span>
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<a href="https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>phyx</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxaa2cdn_example <span class="o" style="font-weight: 600;">&&</span> pxaa2cdn <span class="nt" style="color: #000080;">-a</span> AA_Alignment.fa <span class="nt" style="color: #000080;">-n</span> Unaligned_Nucleotide.fa <span class="nt" style="color: #000080;">-o</span> CDN_aln.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxbdfit_example <span class="o" style="font-weight: 600;">&&</span> pxbdfit <span class="nt" style="color: #000080;">-t</span> bd.tre <span class="nt" style="color: #000080;">-m</span> yule <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cd pxbdsim_example && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file && cd ..</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxboot_example <span class="o" style="font-weight: 600;">&&</span> pxboot <span class="nt" style="color: #000080;">-s</span> Alignment <span class="nt" style="color: #000080;">-x</span> 112233 <span class="nt" style="color: #000080;">-f</span> 0.50 <span class="nt" style="color: #000080;">-o</span> output_of_50_jackknife <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxboot_example <span class="o" style="font-weight: 600;">&&</span> pxboot <span class="nt" style="color: #000080;">-s</span> Alignment <span class="nt" style="color: #000080;">-p</span> parts <span class="nt" style="color: #000080;">-o</span> output_of_bootstrap <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxbp_example <span class="o" style="font-weight: 600;">&&</span> pxbp <span class="nt" style="color: #000080;">-t</span> Tree.tre <span class="nt" style="color: #000080;">-o</span> bp_output <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxcat_example <span class="o" style="font-weight: 600;">&&</span> pxcat <span class="nt" style="color: #000080;">-s</span> <span class="k" style="font-weight: 600;">*</span>.fas <span class="k" style="font-weight: 600;">*</span>.fa <span class="k" style="font-weight: 600;">*</span>.phy <span class="nt" style="color: #000080;">-p</span> Parts.txt <span class="nt" style="color: #000080;">-o</span> Supermatrix.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxclsq_example <span class="o" style="font-weight: 600;">&&</span> pxclsq <span class="nt" style="color: #000080;">-s</span> Alignment <span class="nt" style="color: #000080;">-p</span> 0.6 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxconsq_example <span class="o" style="font-weight: 600;">&&</span> pxconsq <span class="nt" style="color: #000080;">-s</span> Alignment <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
</pre>
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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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxcontrates_example <span class="o" style="font-weight: 600;">&&</span> pxcontrates <span class="nt" style="color: #000080;">-c</span> contrates_file.txt <span class="nt" style="color: #000080;">-t</span> contrates_tree.tre <span class="nt" style="color: #000080;">-a</span> 1 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxfqfilt_example <span class="o" style="font-weight: 600;">&&</span> pxfqfilt <span class="nt" style="color: #000080;">-s</span> fqfilt_test.fastq <span class="nt" style="color: #000080;">-m</span> 10 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
</pre>
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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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlog_example <span class="o" style="font-weight: 600;">&&</span> pxlog <span class="nt" style="color: #000080;">-t</span> <span class="k" style="font-weight: 600;">*</span>.trees <span class="nt" style="color: #000080;">-i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
</pre>
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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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlog_example <span class="o" style="font-weight: 600;">&&</span> pxlog <span class="nt" style="color: #000080;">-t</span> <span class="k" style="font-weight: 600;">*</span>.trees <span class="nt" style="color: #000080;">-b</span> 75 <span class="nt" style="color: #000080;">-n</span> 2 <span class="nt" style="color: #000080;">-o</span> some_output_filename <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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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="shell"></span>
</pre>
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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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlssq_example <span class="o" style="font-weight: 600;">&&</span> pxlssq <span class="nt" style="color: #000080;">-s</span> Alignment <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlstr_example <span class="o" style="font-weight: 600;">&&</span> pxlstr <span class="nt" style="color: #000080;">-t</span> Tree.tre <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrca_example <span class="o" style="font-weight: 600;">&&</span> pxmrca <span class="nt" style="color: #000080;">-t</span> mrca_test.tre <span class="nt" style="color: #000080;">-m</span> mrca.txt <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrcacut_example <span class="o" style="font-weight: 600;">&&</span> pxmrcacut <span class="nt" style="color: #000080;">-t</span> tree <span class="nt" style="color: #000080;">-m</span> mrca_file <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrcaname_example <span class="o" style="font-weight: 600;">&&</span> pxmrcaname <span class="nt" style="color: #000080;">-t</span> tree <span class="nt" style="color: #000080;">-m</span> mrca_file <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxnj_example <span class="o" style="font-weight: 600;">&&</span> pxnj <span class="nt" style="color: #000080;">-s</span> Alignment.aln <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxnw_example <span class="o" style="font-weight: 600;">&&</span> pxnw <span class="nt" style="color: #000080;">-s</span> Alignment.aln <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrecode_example <span class="o" style="font-weight: 600;">&&</span> pxrecode <span class="nt" style="color: #000080;">-s</span> Nucleotide.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrevcomp_example <span class="o" style="font-weight: 600;">&&</span> pxrevcomp <span class="nt" style="color: #000080;">-s</span> Nucleotide.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrls_example <span class="o" style="font-weight: 600;">&&</span> pxrls <span class="nt" style="color: #000080;">-s</span> SeqFile <span class="nt" style="color: #000080;">-c</span> CurrentNames <span class="nt" style="color: #000080;">-n</span> NewNames <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrlt_example <span class="o" style="font-weight: 600;">&&</span> pxrlt <span class="nt" style="color: #000080;">-t</span> kingdoms.tre <span class="nt" style="color: #000080;">-c</span> kingdoms.oldnames.txt <span class="nt" style="color: #000080;">-n</span> kingdoms.newnames.txt <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrms_example <span class="o" style="font-weight: 600;">&&</span> pxrms <span class="nt" style="color: #000080;">-s</span> Nucleotide.fa <span class="nt" style="color: #000080;">-f</span> taxa_to_delete.txt <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"></span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrmt_example <span class="o" style="font-weight: 600;">&&</span> pxrmt <span class="nt" style="color: #000080;">-t</span> rmt_test.tre <span class="nt" style="color: #000080;">-n</span> s1,s6,s8 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrr_example <span class="o" style="font-weight: 600;">&&</span> pxrr <span class="nt" style="color: #000080;">-t</span> rr_test.tre <span class="nt" style="color: #000080;">-g</span> s1,s2 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxs2fa_pxs2phy_pxs2nex_example <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"> pxs2fa <span class="nt" style="color: #000080;">-s</span> Alignment <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"> pxs2phy <span class="nt" style="color: #000080;">-s</span> Alignment <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> pxs2nex <span class="nt" style="color: #000080;">-s</span> Alignment <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxseqgen_example <span class="o" style="font-weight: 600;">&&</span> pxseqgen <span class="nt" style="color: #000080;">-t</span> seqgen_test.tre <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxseqgen_example <span class="o" style="font-weight: 600;">&&</span> pxseqgen <span class="nt" style="color: #000080;">-t</span> tree_file <span class="nt" style="color: #000080;">-o</span> output_alignment <span class="nt" style="color: #000080;">-m</span> .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxsstat_example <span class="o" style="font-weight: 600;">&&</span> pxsstat <span class="nt" style="color: #000080;">-s</span> Alignment.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxstrec_example <span class="o" style="font-weight: 600;">&&</span> pxstrec <span class="nt" style="color: #000080;">-d</span> test.data.narrow <span class="nt" style="color: #000080;">-t</span> test.tre <span class="nt" style="color: #000080;">-c</span> config_stmap <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxsw_example <span class="o" style="font-weight: 600;">&&</span> pxsw <span class="nt" style="color: #000080;">-s</span> Alignment.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"></span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxt2new_example <span class="o" style="font-weight: 600;">&&</span> pxt2new <span class="nt" style="color: #000080;">-t</span> Tree.nex <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"></span>
</pre>
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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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxtlate_example <span class="o" style="font-weight: 600;">&&</span> pxtlate <span class="nt" style="color: #000080;">-s</span> Sequence.fa <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"></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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxtscale_example <span class="o" style="font-weight: 600;">&&</span> pxtscale <span class="nt" style="color: #000080;">-t</span> Tree <span class="nt" style="color: #000080;">-s</span> 2.0 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"></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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxupgma_example <span class="o" style="font-weight: 600;">&&</span> pxupgma <span class="nt" style="color: #000080;">-s</span> drosophila.aln <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"></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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxvcf2fa_example <span class="o" style="font-weight: 600;">&&</span> pxvcf2fa <span class="nt" style="color: #000080;">-s</span> vcf_file <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span></pre>
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