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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pplacer">Debian Med / pplacer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pplacer/-/commit/4283efac81204522fddf1337586815342f25bc26">4283efac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-22T09:05:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pplacer/-/commit/0e64ac7167f17ccf06da66cfdbb489abc9de6dd1">0e64ac71</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-22T09:16:32+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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debian/createmanpages
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<li class="file-stats">
<a href="#27fe1f701b5bf2c596e8a5f9bea8b11c85635116">
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+
debian/guppy.1
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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<li class="file-stats">
<a href="#ec929ef01d1cf2a9933f4a573f16144feabcf330">
debian/patches/fix_makefile.patch
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<li class="file-stats">
<a href="#ac9a0fb7ed09d8775c7899149574abe3381357dd">
debian/patches/ocamlbuild
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<li class="file-stats">
<a href="#bbb0ea7cc9c0396f4b5b2818e2b101ffe5f870bc">
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+
debian/pplacer.1
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<li class="file-stats">
<a href="#51b6089cf425be4ba227d64e73cb4e27e946bcbd">
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+
debian/rppr.1
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<h4>Changes:</h4>
<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"place reads on a phylogenetic tree"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>guppy</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes pplacer output"</span> <span class="se" style="color: #d14;">\</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>rppr</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"tool for working with reference packages"</span> <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#27fe1f701b5bf2c596e8a5f9bea8b11c85635116"><strong>debian/guppy.1</strong></a>
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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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH GUPPY "1" "June 2020" "guppy 1.1~alpha19" "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">guppy \- Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes pplacer output</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B guppy</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><command> [options]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS visualization</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">fat</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">makes trees with edges fattened in proportion to the number of reads</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">heat</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">maps an an arbitrary vector of the correct length to the tree</span>
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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="LC17" class="line" lang="plaintext">sing</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">makes one tree for each query sequence, showing uncertainty</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">tog</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">makes a tree with each of the reads represented as a pendant edge</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SS statistical comparison</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">bary</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">draws the barycenter of a placement collection on the reference tree</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">edpl</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">calculates the EDPL uncertainty values for a collection of pqueries</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">epca</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">performs edge principal components</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">error</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">finds the error between two placefiles</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">fpd</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">calculates various alpha diversity metrics of placefiles</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">indep_c</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">calculates the independent contrasts of pqueries</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">kr</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">calculates the Kantorovich\-Rubinstein distance and corresponding p\-values</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">kr_heat</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">makes a heat tree</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">lpca</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">performs length principal components</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">mcl</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">cluster pqueries using Markov clustering via MCL</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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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">pmlpca</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">performs poor\-man's length principal components</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">rarefact</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">calculates phylogenetic rarefaction curves</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.TP</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">splitify</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">writes out differences of masses for the splits of the tree</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">squash</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">performs squash clustering</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.TP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">unifrac</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">calculates unifrac on two or more placefiles</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.SH classification</span>
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69
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<pre style="margin: 0;">+<span id="LC69" 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">classify</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">outputs classification information in SQLite format</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.TP</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">to_rdp</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">convert a reference package to a format RDP wants</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.SS utilities</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">adcl</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">calculates ADCL for each pquery in a placefile</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.TP</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">check</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">checks placefiles for common problems</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.TP</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">compress</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">compresses a placefile's pqueries</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.TP</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">demulti</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">splits apart placements with multiplicity, undoing a round procedure</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.TP</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">distmat</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">prints out a pairwise distance matrix between the edges</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.TP</span>
</pre>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">filter</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">filters one or more placefiles by placement name</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.TP</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">info</span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">writes the number of leaves of the reference tree and the number of pqueries</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.TP</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">islands</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">finds the mass islands of one or more pqueries</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">merge</span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">merges placefiles together</span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">mft</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">Multi\-Filter and Transform placefiles</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">ograph</span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">finds the overlap graph of one or more pqueries</span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.TP</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">placemat</span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">prints out a pairwise distance matrix between placements</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.TP</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">rarefy</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">performs rarefaction on collections of placements</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.TP</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">redup</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">restores duplicates to deduped placefiles</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.TP</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">round</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">clusters the placements by rounding branch lengths</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.TP</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">to_csv</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">turns a placefile into a csv file</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.TP</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">to_json</span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">converts old\-style .place files to .jplace placement files</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">trim</span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">trims placefiles down to only containing an informative subset of the mass</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.PP</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">To get more help about a given command, type guppy COMMAND \fB\-\-help\fR</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.SS "Additional options"</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.TP</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">\fB\-\-version\fR</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Print version and exit</span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.TP</span>
</pre>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">\fB\-\-cmds\fR</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">Print a list of the available commands.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.TP</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">\fB\-\-batch\fR</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">Run the provided batch file of guppy commands</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">.TP</span>
</pre>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">\fB\-\-quiet\fR</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">Don't write messages to stdout (unless explicitly requested).</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.TP</span>
</pre>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">\fB\-\-help\fR</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">Display this list of options and subcommands</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.TP</span>
</pre>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">\fB\-help\fR</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">Display this list of options and subcommands</span>
</pre>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">.SH AUTHOR</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#ec929ef01d1cf2a9933f4a573f16144feabcf330"><strong>debian/patches/fix_makefile.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 22 May 2020 07:19:29 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Avoid calling git to obtain version</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" 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="LC7" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#ac9a0fb7ed09d8775c7899149574abe3381357dd"><strong>debian/patches/ocamlbuild</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Ralf Treinen </span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Shayan Doust</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-06-21 22:04:51 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: Build with recent ocaml</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- pplacer.orig/myocamlbuild.ml</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;">+++ pplacer/myocamlbuild.ml</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -19,10 +19,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#bbb0ea7cc9c0396f4b5b2818e2b101ffe5f870bc"><strong>debian/pplacer.1</strong></a>
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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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PPLACER "1" "June 2020" "pplacer 1.1~alpha19" "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">pplacer \- place reads on a phylogenetic tree</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B pplacer</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[options] [alignment]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.TP</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\fB\-c\fR</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Specify the path to the reference package.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-t\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Specify the reference tree filename.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-r\fR</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Specify the reference alignment filename.</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-s\fR</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Supply a phyml stats.txt or a RAxML info file giving the model parameters.</span>
</pre>
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<td class="diff-line-num new new_line" 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">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-d\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Specify the directory containing the reference information.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-p\fR</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Calculate posterior probabilities.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-m\fR</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-\-model\-freqs\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Use model frequencies instead of reference alignment frequencies.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-\-gamma\-cats\fR</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Number of categories for discrete gamma model.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-\-gamma\-alpha\fR</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Specify the shape parameter for a discrete gamma model.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-ml\-tolerance\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">1st stage branch len optimization tolerance (2nd stage to 1e\-5). Default: 0.01.</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-pp\-rel\-err\fR</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Relative error for the posterior probability calculation. Default is 0.01.</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-\-unif\-prior\fR</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Use a uniform prior rather than exponential.</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-\-inform\-prior\fR</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Use an informative exponential prior based on rooted distance to leaves.</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-\-prior\-lower\fR</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Lower bound for the informative prior mean. Default is 0.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">\fB\-\-start\-pend\fR</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Starting pendant branch length. Default is 0.1.</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">\fB\-\-max\-pend\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Set the maximum ML pendant branch length. Default is 2.</span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.TP</span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-\-fig\-cutoff\fR</span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">The cutoff for determining figs. Default is 0; specify 0 to disable.</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.TP</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">\fB\-\-fig\-eval\-all\fR</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Evaluate all likelihoods to ensure that the best location was selected.</span>
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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-\-fig\-eval\-discrepancy\-tree\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">Write out a tree showing the discrepancies between the best complete and observed locations.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" 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">\fB\-\-fig\-tree\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Write out a tree showing the figs on the tree.</span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">\fB\-\-max\-strikes\fR</span>
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<td class="diff-line-num new new_line" 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="plaintext">Maximum number of strikes for baseball. 0 \-> no ball playing. Default is 6.</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.TP</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">\fB\-\-strike\-box\fR</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">Set the size of the strike box in log likelihood units. Default is 3.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">\fB\-\-max\-pitches\fR</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">Set the maximum number of pitches for baseball. Default is 40.</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">.TP</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">\fB\-\-fantasy\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Desired likelihood cutoff for fantasy baseball mode. 0 \-> no fantasy.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.TP</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">\fB\-\-fantasy\-frac\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Fraction of fragments to use when running fantasy baseball. Default is 0.1.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">\fB\-\-write\-masked\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">Write alignment masked to the region without gaps in the query.</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.TP</span>
</pre>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">\fB\-\-verbosity\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">\fB\-\-out\-dir\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">Specify the directory to write place files to.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\fB\-o\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">Specify the output file name</span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.TP</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-\-pretend\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Only check out the files then report. Do not run the analysis.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">\fB\-\-check\-like\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">Write out the likelihood of the reference tree, calculated two ways.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">\fB\-j\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">The number of child processes to spawn when doing placements. Default is 2.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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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="LC109" class="line" lang="plaintext">\fB\-\-timing\fR</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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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="LC110" class="line" lang="plaintext">Display timing information after the pplacer run finishes.</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
</td>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">\fB\-\-no\-pre\-mask\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">Don't pre\-mask sequences before placement.</span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">\fB\-\-write\-pre\-masked\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">Write out the pre\-masked sequences to the specified fasta file before placement.</span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">\fB\-\-map\-mrca\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">Specify a file to write out MAP sequences for MRCAs and corresponding placements.</span>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">\fB\-\-map\-mrca\-min\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">Specify cutoff for inclusion in MAP sequence file. Default is 0.8.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.TP</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">\fB\-\-map\-identity\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">Add the percent identity of the query sequence to the nearest MAP sequence to each placement.</span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">\fB\-\-keep\-at\-most\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">The maximum number of placements we keep. Default is 7.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.TP</span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">\fB\-\-keep\-factor\fR</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">Throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01.</span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">\fB\-\-mrca\-class\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">Classify with MRCAs instead of a painted tree.</span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">\fB\-\-groups\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">Split query alignment into the specified number of groups.</span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">\fB\-\-always\-refine\fR</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">Always refine the model before placing.</span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">.TP</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">\fB\-\-mmap\-file\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist.</span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">\fB\-\-discard\-nonoverlapped\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">When pre\-masking, silently discard sequences which don't overlap the mask.</span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">\fB\-\-version\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">Write out the version number and exit.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.TP</span>
</pre>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">\fB\-help\fR</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">Display this list of options</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">.TP</span>
</pre>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">\fB\-\-help\fR</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">Display this list of options</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">.SH AUTHOR</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="51b6089cf425be4ba227d64e73cb4e27e946bcbd">
<a href="https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1#51b6089cf425be4ba227d64e73cb4e27e946bcbd"><strong>debian/rppr.1</strong></a>
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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 1.47.15.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RPPR "1" "June 2020" "rppr 1.1~alpha19" "User Commands"</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">rppr \- tool for working with reference packages</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B rppr</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><command> [options]</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "available commands"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">check</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">checks a reference package</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">convex_taxids</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">determines convex tax_ids per\-rank in a refpkg</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">convexify</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">identifies minimal leaf set to cut for taxonomic concordance</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">infer</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">infers classifications of unclassified sequences in a reference package</span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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">info</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">gives information about a reference package</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">min_adcl</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">finds a good collection of sequences to cut from a placefile's ref tree</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">min_adcl_tree</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">finds a good collection of sequences to cut from a tree</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">pdprune</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">prunes the tree to maximize PD</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">prep_db</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">makes SQL enabling taxonomic querying of placement results</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">prepsim</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">makes a simulation by taking out taxids and turning them into fake placements</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">reclass</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">reclassifies nonconvex sequences in a reference package</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">ref_tree</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">writes a taxonomically annotated reference tree and an induced taxonomic tree</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">reroot</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">reroots a given reference package in place</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.PP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">To get more help about a given command, type rppr COMMAND \fB\-\-help\fR</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.SS "Additional options"</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-\-version\fR</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Print version and exit</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-\-cmds\fR</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Print a list of the available commands.</span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-\-batch\fR</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">Run the provided batch file of guppy commands</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-\-quiet\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Don't write messages to stdout (unless explicitly requested).</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">\fB\-\-help\fR</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Display this list of options and subcommands</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-help\fR</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Display this list of options and subcommands</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.SH AUTHOR</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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