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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/phyx">Debian Med / phyx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/c350e8b1125bdf3a4c1acf171030ac4efea31d0b">c350e8b1</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-09-11T20:05:20Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Redirect output of tests, just print test name, fix dirname
</pre>
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<h4>1 changed file:</h4>
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/phyx/commit/c350e8b1125bdf3a4c1acf171030ac4efea31d0b#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,82 +12,82 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxaa2cdn_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxaa2cdn </span><span class="nt" style="color: #000080;"><span class="idiff">-a</span></span><span class="idiff"> AA_Alignment.fa </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> Unaligned_Nucleotide.fa </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff right"> CDN_aln.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxaa2cdn_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxaa2cdn </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxaa2cdn </span><span class="nt" style="color: #000080;"><span class="idiff">-a</span></span><span class="idiff"> AA_Alignment.fa </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> Unaligned_Nucleotide.fa </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> CDN_aln.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxbdfit_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxbdfit </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> bd.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> yule</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="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">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxbdfit_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxbdfit </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxbdfit </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> bd.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff"> yule </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cd pxbdsim_example && <span class="idiff left right">pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file</span> && cd ..</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cd pxbdsim_example && <span class="idiff left right">echo pxbdsim && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file >/dev/null</span> && cd ..</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxboot_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxboot </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-x</span></span><span class="idiff"> 112233 </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff"> 0.50 </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff right"> output_of_50_jackknife</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxboot_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxboot </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxboot </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-x</span></span><span class="idiff"> 112233 </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff"> 0.50 </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> output_of_50_jackknife </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxboot_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxboot </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-p</span></span><span class="idiff"> parts </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff right"> output_of_bootstrap</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxboot_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxboot </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxboot </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-p</span></span><span class="idiff"> parts </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> output_of_bootstrap </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxbp_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxbp </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> Tree.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff right"> bp_output</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxbp_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxbp </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxbp </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> Tree.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> bp_output </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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27
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<td class="diff-line-num new_line old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxcat_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxcat </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.fas </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.fa </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.phy </span><span class="nt" style="color: #000080;"><span class="idiff">-p</span></span><span class="idiff"> Parts.txt </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff right"> Supermatrix.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxcat_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxcat </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxcat </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.fas </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.fa </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.phy </span><span class="nt" style="color: #000080;"><span class="idiff">-p</span></span><span class="idiff"> Parts.txt </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> Supermatrix.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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28
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxclsq_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxclsq </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-p</span></span><span class="idiff right"> 0.6</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxclsq_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxclsq </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxclsq </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-p</span></span><span class="idiff"> 0.6 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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30
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxconsq_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxconsq </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxconsq_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxconsq </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxconsq </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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32
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxcontrates_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxcontrates </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> contrates_file.txt </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> contrates_tree.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-a</span></span><span class="idiff right"> 1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxcontrates_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxcontrates </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxcontrates </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> contrates_file.txt </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> contrates_tree.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-a</span></span><span class="idiff"> 1 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null 2>/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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34
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxfqfilt_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxfqfilt </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> fqfilt_test.fastq </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> 10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxfqfilt_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxfqfilt </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxfqfilt </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> fqfilt_test.fastq </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff"> 10 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlog_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxlog </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.trees </span><span class="nt" style="color: #000080;"><span class="idiff right">-i</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlog_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxlog </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxlog </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.trees </span><span class="nt" style="color: #000080;"><span class="idiff">-i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlog_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxlog </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.trees </span><span class="nt" style="color: #000080;"><span class="idiff">-b</span></span><span class="idiff"> 75 </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> 2 </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff right"> some_output_filename</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlog_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxlog </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxlog </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.trees </span><span class="nt" style="color: #000080;"><span class="idiff">-b</span></span><span class="idiff"> 75 </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> 2 </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> some_output_filename </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlssq_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxlssq </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlssq_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxlssq </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxlssq </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"></span>
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43
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<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlstr_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxlstr </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff right"> Tree.tre</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxlstr_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxlstr </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxlstr </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> Tree.tre </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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44
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrca_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxmrca </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> mrca_test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> mrca.txt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrca_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxmrca </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxmrca </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> mrca_test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff"> mrca.txt </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrcacut_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxmrcacut </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> tree </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> mrca_file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrcacut_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxmrcacut </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxmrcacut </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> tree </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff"> mrca_file </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrcaname_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxmrcaname </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> tree </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> mrca_file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxmrcaname_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxmrcaname </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxmrcaname </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> tree </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff"> mrca_file </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxnj_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxnj </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment.aln</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxnj_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxnj </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxnj </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment.aln </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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52
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxnw_example<span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxnw </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment.aln</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxnw_example<span class="idiff left">s </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">echo </span></span><span class="idiff">pxnw </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxnw </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment.aln </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrecode_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrecode </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Nucleotide.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrecode_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrecode </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrecode </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Nucleotide.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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56
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"></span>
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57
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<td class="diff-line-num new_line old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrevcomp_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrevcomp </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Nucleotide.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrevcomp_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrevcomp </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrevcomp </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Nucleotide.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrls_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrls </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> SeqFile </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> CurrentNames </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff right"> NewNames</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrls_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrls </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrls </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> SeqFile </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> CurrentNames </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> NewNames </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrlt_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrlt </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> kingdoms.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> kingdoms.oldnames.txt </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff right"> kingdoms.newnames.txt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrlt_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrlt </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrlt </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> kingdoms.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> kingdoms.oldnames.txt </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> kingdoms.newnames.txt </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrms_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrms </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Nucleotide.fa </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff right"> taxa_to_delete.txt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrms_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrms </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrms </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Nucleotide.fa </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff"> taxa_to_delete.txt </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrmt_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrmt </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> rmt_test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff right"> s1,s6,s8</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrmt_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrmt </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrmt </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> rmt_test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> s1,s6,s8 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrr_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxrr </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> rr_test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="idiff right"> s1,s2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxrr_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxrr </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxrr </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> rr_test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="idiff"> s1,s2 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxs2fa_pxs2phy_pxs2nex_example <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="shell"> <span class="idiff left">pxs2fa </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"> <span class="idiff left">pxs2phy </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell"> <span class="idiff left">pxs2nex </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxs2fa </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxs2fa </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxs2phy </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxs2phy </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxs2nex </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxs2nex </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxseqgen_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxseqgen </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff right"> seqgen_test.tre</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxseqgen_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxseqgen </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxseqgen </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> seqgen_test.tre </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxseqgen_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxseqgen </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> tree_file </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> output_alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxseqgen_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxseqgen </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxseqgen </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> tree_file </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> output_alignment </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff"> .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxsstat_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxsstat </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="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="shell"><span class="nb" style="color: #0086b3;">cd </span>pxsstat_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxsstat </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxsstat </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxstrec_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxstrec </span><span class="nt" style="color: #000080;"><span class="idiff">-d</span></span><span class="idiff"> test.data.narrow </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff right"> config_stmap</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxstrec_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxstrec </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxstrec </span><span class="nt" style="color: #000080;"><span class="idiff">-d</span></span><span class="idiff"> test.data.narrow </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> test.tre </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> config_stmap </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxsw_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxsw </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Alignment.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxsw_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxsw </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxsw </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Alignment.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxt2new_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxt2new </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff right"> Tree.nex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxt2new_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxt2new </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxt2new </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> Tree.nex </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxtlate_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxtlate </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> Sequence.fa</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxtlate_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxtlate </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxtlate </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> Sequence.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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88
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxtscale_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxtscale </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> Tree </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> 2.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxtscale_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxtscale </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxtscale </span><span class="nt" style="color: #000080;"><span class="idiff">-t</span></span><span class="idiff"> Tree </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> 2.0 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxupgma_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxupgma </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> drosophila.aln</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxupgma_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxupgma </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxupgma </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> drosophila.aln </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxvcf2fa_example <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">pxvcf2fa </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> vcf_file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span></pre>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pxvcf2fa_example <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">pxvcf2fa </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> pxvcf2fa </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> vcf_file </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span></pre>
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