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_sources/usage/index.rst.txt

@@ -87,7 +87,7 @@ To report inparalogs and specify which was kept per SNAP-OG, use the -rih, \-\-r
 argument. The resulting file, which will have the suffix ".inparalog_report.txt," will have three columns: |br|
 - col 1 is the orthogroup file |br|
 - col 2 is the inparalog that was kept |br|
-- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";" |br|
+- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";"
 
 To generate this file, use the following command:
 
@@ -125,3 +125,8 @@ All options
 +-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
 *For genome-scale analyses, we recommend changing the -o/\-\-occupancy parameter to be the same for all large gene families so that the minimum SNAP-OG occupancy is the same
 for all SNAP-OGs.
+
+
+.. |br| raw:: html
+
+  <br/>

usage/index.html

@@ -238,10 +238,10 @@ <h2>Specifying which inparalog to keep<a class="headerlink" href="#specifying-wh
 <div class="section" id="report-inparalog-handling">
 <h2>Report inparalog handling<a class="headerlink" href="#report-inparalog-handling" title="Permalink to this headline">¶</a></h2>
 <p>To report inparalogs and specify which was kept per SNAP-OG, use the -rih, --report_inparalog_handling
-argument. The resulting file, which will have the suffix “.inparalog_report.txt,” will have three columns: <a href="#id3"><span class="problematic" id="id4">|br|</span></a>
-- col 1 is the orthogroup file <a href="#id5"><span class="problematic" id="id6">|br|</span></a>
-- col 2 is the inparalog that was kept <a href="#id7"><span class="problematic" id="id8">|br|</span></a>
-- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon “;” <a href="#id9"><span class="problematic" id="id10">|br|</span></a></p>
+argument. The resulting file, which will have the suffix “.inparalog_report.txt,” will have three columns: <br/>
+- col 1 is the orthogroup file <br/>
+- col 2 is the inparalog that was kept <br/>
+- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon “;”</p>
 <p>To generate this file, use the following command:</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -rih
 </pre></div>