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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/roguenarok">Debian Med / roguenarok</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/e9bf725a927f77965ae29e5641b9cb60f4371698">e9bf725a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T20:05:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove d/tests/data since upstream vendors the same as example in source
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/d6e490d04fb638d037a63e788b3bd7280231067a">d6e490d0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T20:06:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/examples: Install examples/* instead
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/389cd835a19c1843bba96eb02181d3323baa444c">389cd835</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T20:17:55+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/p/hardening.patch: Append options to CFLAGS and pass hardening options properly to vendor dbg and fix blhc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/82e3fca76c50624fdca59ea9cbb3e3b44e293d0b">82e3fca7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T20:21:22+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: s/make/$(MAKE)/g
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/b6756852ce8a3e72053694ce851cda2f72409588">b6756852</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T15:27:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/p/fix-manpage-call-and-help-exit-code.patch
* Help option path is called with a relative path in current dir, remove the relative dir
* Exits with abort() after printing help, exit with 0 instead
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/646f5a555ed9f8d485afeb2edbc651376f0f5995">646f5a55</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T15:27:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2">c5dba1bc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-07T20:59:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
debian/examples
</a>
</li>
<li class="file-stats">
<a href="#239fca29288131b8587b5a7ec89a761b941f53b8">
debian/mans/rnr-lsi.1
</a>
</li>
<li class="file-stats">
<a href="#9c236caf44da42095fb3e3058aa442c7293124e9">
debian/mans/rnr-mast.1
</a>
</li>
<li class="file-stats">
<a href="#ecf40c03f536434ea5bb3e92a639e5ab540cebc7">
debian/mans/rnr-prune.1
</a>
</li>
<li class="file-stats">
<a href="#a9647b7b8e6d1109b7a8a67a6d9234a72825bed4">
debian/mans/rnr-tii.1
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</li>
<li class="file-stats">
<a href="#ce6813a90277a4798a2426c9b571bab3d192d177">
debian/mans/roguenarok-parallel.1
</a>
</li>
<li class="file-stats">
<a href="#ee11af950b95fffd8f0ec32cd6e9ab5ee1fc31c7">
debian/mans/roguenarok-single.1
</a>
</li>
<li class="file-stats">
<a href="#55dd8a038e23746a57041fbd04e0794f37519b2e">
<span class="new-file">
+
debian/patches/fix-manpage-call-and-help-exit-code.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#e6e724810c06058f380205bfbb699611933e2170">
<span class="deleted-file">
−
debian/tests/data/150.bs
</span>
</a>
</li>
<li class="file-stats">
<a href="#5a972889af05ccc126cc64d61f0f662f1e4ccded">
<span class="deleted-file">
−
debian/tests/data/150.tre
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">roguenarok (1.0.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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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"> * Remove d/tests/data since upstream vendors the same as example in source</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * d/examples: Install examples/* instead</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/p/hardening.patch: Append options to CFLAGS and pass hardening</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> options properly to vendor dbg and fix blhc</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * d/rules: s/make/$(MAKE)/g</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * d/p/fix-manpage-call-and-help-exit-code.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> + Help option path is called with a relative path in current</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> dir, remove the relative dir path in help display</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> + Exits with abort() after printing help, exit with 0 instead</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Update manpages</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Thu, 07 Oct 2021 20:22:14 +0530</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">roguenarok (1.0.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">example/*</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#239fca29288131b8587b5a7ec89a761b941f53b8"><strong>debian/mans/rnr-lsi.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH RNR-LSI "1" "March 2017" "rnr-lsi 1.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RNR-LSI "1" "October 2021" "rnr-lsi 1.0.1" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">rnr-lsi \- computes three flavors of leaf stability index for each taxon</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B rnr\-lsi</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">.SS OBLIGATORY</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">This is RnR\-lsi version 1.0.1 released by Andre J. Aberer in 2021\-06\-07.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">This program computes three flavors of leaf stability index for each taxon.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">SYNTAX: rnr\-lsi \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">OBLIGATORY:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.PP</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">\fB\-i\fR <bootTrees></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.IP</span>
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11
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">A collection of bootstrap trees.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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13
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">\fB\-n\fR <runId></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.IP</span>
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14
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">An identifier for this run.</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.SS OPTIONAL</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">OPTIONAL:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.PP</span>
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17
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">\fB\-x\fR <excludeFile></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.IP</span>
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18
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Prune the taxa in the file first (one taxon per line), before computing the lsi.</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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20
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">\fB\-w\fR <workDir></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.IP</span>
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21
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">A working directory where output files are created.</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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23
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">\fB\-h\fR</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.IP</span>
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24
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">This help file.</span>
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25
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Andreas Tille</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Nilesh Patra</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#9c236caf44da42095fb3e3058aa442c7293124e9"><strong>debian/mans/rnr-mast.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH RNR-MAST "1" "March 2017" "rnr-mast 1.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RNR-MAST "1" "October 2021" "rnr-mast 1.0.1" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">rnr-mast \- computes maximum agreement trees for unrooted input sets</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B rnr\-mast</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-a] [\-x <excludeFile>]</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">.SS OBLIGATORY</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">This is RnR\-mast version 1.0 released by Andre J. Aberer in 2011\-10\-25.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">This program computes maximum agreement trees for unrooted input sets.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">SYNTAX: rnr\-mast \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-a] [\-x <excludeFile>]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">OBLIGATORY:</span>
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10
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">\fB\-i\fR <bootTrees></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.IP</span>
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11
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">A collection of bootstrap trees.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">\fB\-n\fR <runId></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">An identifier for this run.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.<span class="idiff left right">SS OPTIONAL</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">.TP</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"><span class="idiff left right">OPTIONAL</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">\fB\-a\fR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Compute all possible MAST trees. Without this flag, you will</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">only get a few MASTs that are easy to compute. As there may be an</span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">exponential number of MASTs, use this option with care.</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">\fB\-w\fR <workDir></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.IP</span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">A working directory where output files are created.</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">\fB\-x\fR <excludeFile></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Exclude the taxa in this file (one taxon per line)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">prior to computing the MAST. If you compute all MASTs anyway, this</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">option is option will not be useful. However, you can use this option</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">to speed up things.</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">\fB\-h\fR</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">This help file.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Andreas Tille</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Nilesh Patra</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#ecf40c03f536434ea5bb3e92a639e5ab540cebc7"><strong>debian/mans/rnr-prune.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH RNR-PRUNE "1" "March 2017" "rnr-prune 1.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RNR-PRUNE "1" "October 2021" "rnr-prune 1.0.1" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">rnr-prune \- prunes a list of taxa from a bootstrap tree or a single tree with branch lengths</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B rnr\-prune</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">[\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">This is RnR\-prune version 1.0 released by Andre J. Aberer in 2011\-10\-25.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best\-known ML/MP\-tree).</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.SS OBLIGATORY</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">.TP</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">SYNTAX: rnr\-prune [\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">OBLIGATORY:</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.PP</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">\fB\-x\fR <excludeFile></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.IP</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">A list of taxa (one taxon per line) to prune from either the bootstrap trees or the single best\-known tree.</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">\fB\-i\fR <bootTrees></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.IP</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">A collection of bootstrap trees.</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">\fB\-t\fR <treeFile></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">A single tree with branch lengths. Use either this flag or the \fB\-i\fR flag.</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">\fB\-n\fR <runId></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">An identifier for this run.</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">.SS OPTIONAL</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">.TP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">OPTIONAL:</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.PP</span>
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25
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">\fB\-w\fR <workDir></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.IP</span>
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26
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">A working directory where output files are created.</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">\fB\-h\fR</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">This help file.</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Andreas Tille</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Nilesh Patra</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="a9647b7b8e6d1109b7a8a67a6d9234a72825bed4">
<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#a9647b7b8e6d1109b7a8a67a6d9234a72825bed4"><strong>debian/mans/rnr-tii.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH RNR-TII "1" "March 2017" "rnr-tii 1.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RNR-TII "1" "October 2021" "rnr-tii 1.0.1" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">rnr-tii \- computes the taxonomic instability index</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B rnr\-tii</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.SH OPTIONS</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">.SS OBLIGATORY</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.TP</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">This is RnR\-tii version 1.0 released by Andre J. Aberer in 2011\-10\-25.</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">This program computes the taxonomic instability index.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">SYNTAX: rnr\-tii \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">OBLIGATORY:</span>
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10
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">\fB\-i\fR <bootTrees></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.IP</span>
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11
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">A collection of bootstrap trees.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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13
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">\fB\-n\fR <runId></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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14
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">An identifier for this run.</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.<span class="idiff left right">SS OPTIONAL</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">.TP</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"><span class="idiff left right">OPTIONAL</span></span>
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17
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">\fB\-z\fR <z></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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18
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">The exponent used in the TII formula. Use small values to emphasize close relationships and vice versa. DEFAULT: 2</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">\fB\-w\fR <workDir></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">A working directory where output files are created.</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">\fB\-x\fR <excludeFile></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Exclude the taxa in this file (one taxon per line) prior to computing the TII.</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">\fB\-h\fR</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">This help file.</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">.SH AUTHOR</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Andreas Tille</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">This manpage was written by <span class="idiff left right">Nilesh Patra</span> for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="ce6813a90277a4798a2426c9b571bab3d192d177">
<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#ce6813a90277a4798a2426c9b571bab3d192d177"><strong>debian/mans/roguenarok-parallel.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH ROGUENAROK-PARALLEL "1" "March 2017" "roguenarok-parallel 1.0" "User Commands"</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH ROGUENAROK-PARALLEL "1" "October 2021" "roguenarok-parallel 1.0.1" "User Commands"</span>
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2
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">roguenarok-parallel \- implements the RogueNaRok algorithm for rogue taxon identification (parallel version)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B roguenarok-parallel</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.SH OPTIONS</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">.SS OBLIGATORY</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">roguenarok\-parallel: invalid option \fB\-\-\fR '\-'</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011\-10\-25.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">This program implements the RogueNaRok algorithm for rogue taxon identification.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">SYNTAX: RogueNaRok \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">OBLIGATORY:</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.PP</span>
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10
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">\fB\-i\fR <bootTrees></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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11
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">A collection of bootstrap trees.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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13
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">\fB\-n\fR <runId></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
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14
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">An identifier for this run.</span>
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<td class="old_line diff-line-num old" data-linenumber="15" 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">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.TP</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">\fB\-T\fR <num></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Execute RogueNaRok in parallel with <num> threads.</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">.SS OPTIONAL</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">.TP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">OPTIONAL:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">\fB\-t\fR <bestKnownTree></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">If a single best\-known tree (such as an ML or MP</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">tree) is provided, RogueNaRok optimizes the bootstrap support in this</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">best\-known tree (still drawn from the bootstrap trees). The threshold</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">parameter is ignored.</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">\fB\-x\fR <excludeFile></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">taxa in this file (one taxon per line) will not be</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">considered for pruning.</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">\fB\-c\fR <threshold></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">A threshold or mode for the consensus tree that is</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">optimized. Specify a value between 50 (majority rule consensus) and</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">100 (strict consensus) or MR (for the extended majority rule</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">consensus). Note that rogue taxa identified with respect to different</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">thresholds can vary substantially. DEFAULT: MR consensus</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">\fB\-b\fR</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Instead of trying to maximize the support in the consensus tree,</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">the RogueNaRok will try to maximize the number of bipartition in the</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">final tree by pruning taxa. DEFAULT: off</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">\fB\-L\fR <factor></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">a weight factor to penalize for dropset size.</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Factor=1 is Pattengale's criterion. The higher the value, the more</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC)</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">\fB\-s\fR <dropsetSize></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">maximum size of dropset per iteration. If</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">dropsetSize == n, then RogueNaRok will test in each iteration which</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">tuple of n taxa increases optimality criterion the most and prunes</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">taxa accordingly. This improves the result, but runtimes will</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">increase at least linearly. DEFAULT: 1</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">\fB\-w\fR <workDir></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">A working directory where output files are created.</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">.TP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.PP</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-T\fR <num></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.IP</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Execute RogueNaRok in parallel with <num> threads. You need to compile the program for parallel execution first.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.PP</span>
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57
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">\fB\-h\fR</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">This help file.</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">.SH EXAMPLES</span>
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60
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">.IP</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">roguenarok-parallel -T2 \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">This help file.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.PP</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">MINIMAL EXAMPLE:</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1</span>
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62
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">.SH AUTHOR</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">RogueNaRok was released by Andre J. Aberer in 2011\-10\-25.</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">.P</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="ee11af950b95fffd8f0ec32cd6e9ab5ee1fc31c7">
<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#ee11af950b95fffd8f0ec32cd6e9ab5ee1fc31c7"><strong>debian/mans/roguenarok-single.1</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH ROGUENAROK-SINGLE "1" "March 2017" "roguenarok-single 1.0" "User Commands"</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH ROGUENAROK-SINGLE "1" "October 2021" "roguenarok-single 1.0.1" "User Commands"</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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3
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">roguenarok-single \- implements the RogueNaRok algorithm for rogue taxon identification (single core version)</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B roguenarok-single</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.SH OPTIONS</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">.SS OBLIGATORY</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.TP</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ERROR: Please specify a file containing bootstrap trees via \fB\-i\fR.</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011\-10\-25.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">This program implements the RogueNaRok algorithm for rogue taxon identification.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">SYNTAX: RogueNaRok \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">OBLIGATORY:</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.PP</span>
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10
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">\fB\-i\fR <bootTrees></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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11
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<td class="new_line diff-line-num" 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="plaintext">A collection of bootstrap trees.</span>
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<td class="old_line diff-line-num old" data-linenumber="12" 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">
12
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<td class="new_line diff-line-num old" data-linenumber="19" 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="LC12" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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13
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">\fB\-n\fR <runId></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="new_line diff-line-num" data-linenumber="22" 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">
22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">An identifier for this run.</span>
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<td class="old_line diff-line-num old" data-linenumber="15" 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">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.SS OPTIONAL</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">OPTIONAL:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">\fB\-t\fR <bestKnownTree></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">If a single best\-known tree (such as an ML or MP</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">tree) is provided, RogueNaRok optimizes the bootstrap support in this</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">best\-known tree (still drawn from the bootstrap trees). The threshold</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">parameter is ignored.</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">\fB\-x\fR <excludeFile></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">taxa in this file (one taxon per line) will not be</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">considered for pruning.</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">\fB\-c\fR <threshold></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">A threshold or mode for the consensus tree that is</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">optimized. Specify a value between 50 (majority rule consensus) and</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">100 (strict consensus) or MR (for the extended majority rule</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">consensus). Note that rogue taxa identified with respect to different</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">thresholds can vary substantially. DEFAULT: MR consensus</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">\fB\-b\fR</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Instead of trying to maximize the support in the consensus tree,</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">the RogueNaRok will try to maximize the number of bipartition in the</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">final tree by pruning taxa. DEFAULT: off</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">\fB\-L\fR <factor></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">a weight factor to penalize for dropset size.</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Factor=1 is Pattengale's criterion. The higher the value, the more</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC)</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">\fB\-s\fR <dropsetSize></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">maximum size of dropset per iteration. If</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">dropsetSize == n, then RogueNaRok will test in each iteration which</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">tuple of n taxa increases optimality criterion the most and prunes</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">taxa accordingly. This improves the result, but runtimes will</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">increase at least linearly. DEFAULT: 1</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">.<span class="idiff left right">T</span>P</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.<span class="idiff left right">P</span>P</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">\fB\-w\fR <workDir></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.IP</span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">A working directory where output files are created.</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">.TP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.PP</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-T\fR <num></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.IP</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Execute RogueNaRok in parallel with <num> threads. You need to compile the program for parallel execution first.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.PP</span>
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54
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">\fB\-h\fR</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">This help file.</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">.SH EXAMPLES</span>
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57
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">.IP</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">roguenarok-single \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">This help file.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.PP</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">MINIMAL EXAMPLE:</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1</span>
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59
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">.SH AUTHOR</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">RogueNaRok was released by Andre J. Aberer in 2011\-10\-25.</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">.P</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="55dd8a038e23746a57041fbd04e0794f37519b2e">
<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#55dd8a038e23746a57041fbd04e0794f37519b2e"><strong>debian/patches/fix-manpage-call-and-help-exit-code.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: This does two things</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> * Help option path is called with a relative path in current dir, remove the relative dir</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> * Exits with abort() after printing help, exit with 0 instead</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-10-07</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/RogueNaRok.c</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/RogueNaRok.c</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -2107,7 +2107,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> void printHelpFile()</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> printVersionInfo(FALSE);</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("This program implements the RogueNaRok algorithm for rogue taxon identification.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-x <excludeFile>] [-c <threshold>] [-b] [-s <dropsetSize>] [-w <workingDir>] [-h]\n", programName);</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf("This program implements the RogueNaRok algorithm for rogue taxon identification.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-x <excludeFile>] [-c <threshold>] [-b] [-s <dropsetSize>] [-w <workingDir>] [-h]\n", programName);</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> printf("\n\tOBLIGATORY:\n");</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> printf("-n <runId>\n\tAn identifier for this run.\n");</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -2219,7 +2219,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> default: </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> printHelpFile();</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- abort ();</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;">+ exit(0);</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/rnr-lsi.c</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/rnr-lsi.c</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -327,7 +327,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> void printHelpFile()</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> {</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> printVersionInfo(FALSE);</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("This program computes three flavors of leaf stability index for each taxon.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf("This program computes three flavors of leaf stability index for each taxon.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> printf("\n\tOBLIGATORY:\n");</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> printf("-n <runId>\n\tAn identifier for this run.\n");</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -372,7 +372,7 @@</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> default: </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> {</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> printHelpFile();</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- abort ();</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit(0);</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> }</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> }</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> }</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/rnr-mast.c</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/rnr-mast.c</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -873,7 +873,7 @@</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> void printHelpFile()</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> {</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> printVersionInfo(FALSE);</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("This program computes maximum agreement trees for unrooted input sets.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-a] [-x <excludeFile>]\n", lowerTheString(programName));</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf("This program computes maximum agreement trees for unrooted input sets.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-a] [-x <excludeFile>]\n", lowerTheString(programName));</span></span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> printf("\nOBLIGATORY:\n");</span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> printf("-n <runId>\n\tAn identifier for this run.\n");</span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"><span class="p">@@ -929,7 +929,7 @@</span></span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> default: </span>
</pre>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> {</span>
</pre>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> printHelpFile();</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- abort ();</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit(0);</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"> }</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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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="LC64" class="line" lang="diff"> }</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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65
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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="LC65" class="line" lang="diff"> }</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/rnr-prune.c</span></span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/rnr-prune.c</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -140,7 +140,7 @@</span></span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> static void printHelpFile()</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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71
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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="LC71" class="line" lang="diff"> printVersionInfo(FALSE);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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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="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best-known ML/MP-tree).\n\nSYNTAX: ./%s [-i <bootTrees> | -t <treeFile>] -x <excludeFile> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf("This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best-known ML/MP-tree).\n\nSYNTAX: %s [-i <bootTrees> | -t <treeFile>] -x <excludeFile> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> printf("\n\tOBLIGATORY:\n");</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> printf("-x <excludeFile>\n\tA list of taxa (one taxon per line) to prune from either the bootstrap trees or the single best-known tree.\n");</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="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="diff"> printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -189,7 +189,7 @@</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> default:</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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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="LC79" class="line" lang="diff"> {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> printHelpFile();</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- abort();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit(0);</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> }</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> }</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> }</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/rnr-tii.c</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/rnr-tii.c</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -245,7 +245,7 @@</span></span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> void printHelpFile()</span>
</pre>
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90
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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="LC90" class="line" lang="diff"> { </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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91
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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="LC91" class="line" lang="diff"> printVersionInfo(FALSE);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("This program computes the taxonomic instability index.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-x <excludeFile>]\n", lowerTheString(programName));</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf("This program computes the taxonomic instability index.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-x <excludeFile>]\n", lowerTheString(programName));</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"> printf("\nOBLIGATORY:\n");</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> printf("-n <runId>\n\tAn identifier for this run.\n");</span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"><span class="p">@@ -293,7 +293,7 @@</span></span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> default: </span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"> {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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="diff"> printHelpFile();</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- abort ();</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit(0);</span></span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> }</span>
</pre>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> }</span>
</pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</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">@@ -7,7 +7,15 @@ Last-Update: 2017-05-01</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">--- a/Makefile</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;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -12,12 +12,12 @@</span> ifeq ($(mode), profile)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> CC = gcc </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -Wall -D_GNU_SOURCE</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -Wall -D_GNU_SOURCE</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> LFLAGS = -lm</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ifeq ($(mode), debug)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -12,12 +12,12 @@</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> ifeq ($(mode), parallel)</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">@@ -23,7 +31,7 @@ Last-Update: 2017-05-01</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> RM = rm -fr</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -33,24 +33,24 @@</span><span class="idiff left right"> mast-objs = rnr-mast.o common.o List.o T</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -33,24 +33,24 @@</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> prune-objs = rnr-prune.o common.o Tree.o BitVector.o HashTable.o legacy.o newFunctions.o List.o</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> rnr-lsi: $(lsi-objs)</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">@@ -51,7 +59,7 @@ Last-Update: 2017-05-01</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> %.o : %.c $(DEPS)</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -c -o $@ $< $(CFLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) <span class="idiff left right">-c -o $@ $< </span>$(CPPFLAGS) $(CFLAGS) $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) $(CFLAGS) <span class="idiff left right">-c -o $@ $< </span>$(LDFLAGS)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> clean : </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> $(RM) $(rnr-objs) $(lsi-objs) $(tii-objs) $(mast-objs) $(prune-objs) $(TARGETS) $(TESTS) $(rnr-test-objs) RogueNaRok-parallel</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix-gcc10-build.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix-manpage-call-and-help-exit-code.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -10,6 +10,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> mv RogueNaRok roguenarok-single</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right">make</span> clean</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right">$(MAKE)</span> clean</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_auto_build -- mode=parallel</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> mv RogueNaRok-parallel roguenarok-parallel</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#e6e724810c06058f380205bfbb699611933e2170"><strong>debian/tests/data/150.bs</strong>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2#5a972889af05ccc126cc64d61f0f662f1e4ccded"><strong>debian/tests/data/150.tre</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" 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