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JLSteenwyk · Feb 6, 2024 · cab0734 · cab0734
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diff --git a/_sources/advanced/index.rst.txt b/_sources/advanced/index.rst.txt
@@ -115,6 +115,24 @@ Output file with the suffix '.clipkit.complementary'
 
 |
 
+.. _Codon:
+
+Codon
+-----
+
+Trims codon-based alignments. If one position in a codon should be trimmed, the whole
+codon will be trimmed. To conduct codon-based trimming, use the -co/\\-\\-codon argument.
+
+.. code-block:: shell
+
+	clipkit <input> --codon
+
+    # or
+
+	clipkit <input> --co
+
+|
+
 .. _`Sequence Type`:
 
 Sequence Type
@@ -151,23 +169,25 @@ All options
 +-----------------------------+-------------------------------------------------------------------+
 | Option                      | Usage and meaning                                                 |
 +=============================+===================================================================+
-| -h/\\-\\-help                 | Print help message                                                |
+| -h/\\-\\-help               | Print help message                                                |
++-----------------------------+-------------------------------------------------------------------+
+| -v/\\-\\-version            | Print software version                                            |
 +-----------------------------+-------------------------------------------------------------------+
-| -v/\\-\\-version              | Print software version                                            |
+| -m/\\-\\-mode               | Specify trimming mode (default: smart-gap)                        |
 +-----------------------------+-------------------------------------------------------------------+
-| -m/\\-\\-mode                 | Specify trimming mode (default: smart-gap)                        |
+| -o/\\-\\-output             | Specify output file name                                          |
 +-----------------------------+-------------------------------------------------------------------+
-| -o/\\-\\-output               | Specify output file name                                          |
+| -g/\\-\\-gaps               | Specify gappyness threshold (between 0 and 1). *Default: 0.9*     |
 +-----------------------------+-------------------------------------------------------------------+
-| -g/\\-\\-gaps                 | Specify gappyness threshold (between 0 and 1). *Default: 0.9*     |
+| -co/\\-\\-codon             | Codon codon-based trimming. *Default: off*                        |
 +-----------------------------+-------------------------------------------------------------------+
-| -if/\\-\\-input_file_format   | Specify input file format*. *Default: auto-detect*                |
+| -if/\\-\\-input_file_format | Specify input file format*. *Default: auto-detect*                |
 +-----------------------------+-------------------------------------------------------------------+
-| -of/\\-\\-output_file_format  | Specify output file format*. *Default: input file type*           |
+| -of/\\-\\-output_file_format| Specify output file format*. *Default: input file type*           |
 +-----------------------------+-------------------------------------------------------------------+
-| -l/\\-\\-log                  | Create a log file. *Default: off*                                 |
+| -l/\\-\\-log                | Create a log file. *Default: off*                                 |
 +-----------------------------+-------------------------------------------------------------------+
-| -c/\\-\\-complementary          | Create a complementary alignment file. *Default: off*             |
+| -c/\\-\\-complementary      | Create a complementary alignment file. *Default: off*             |
 +-----------------------------+-------------------------------------------------------------------+
 
 

diff --git a/_sources/change_log/index.rst.txt b/_sources/change_log/index.rst.txt
@@ -8,6 +8,10 @@ Change log
 
 Major changes to ClipKIT are summarized here.
 
+**2.1.2**
+Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode
+being used, the whole codon will get trimmed from the alignment.
+
 **1.4.0**
 new argument for specifying if sequences are amino acids or nucleotides
 

diff --git a/advanced/index.html b/advanced/index.html
@@ -93,6 +93,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#id2">Output</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#log">Log</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#complementary">Complementary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#codon">Codon</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#sequence-type">Sequence Type</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#all-options">All options</a></li>
 </ul>
@@ -268,8 +269,23 @@ <h2>Output<a class="headerlink" href="#id2" title="Permalink to this headline">
 <div class="line"><br /></div>
 </div>
 </div>
+<div class="section" id="codon">
+<span id="id5"></span><h2>Codon<a class="headerlink" href="#codon" title="Permalink to this headline">¶</a></h2>
+<p>Trims codon-based alignments. If one position in a codon should be trimmed, the whole
+codon will be trimmed. To conduct codon-based trimming, use the -co/--codon argument.</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>    clipkit &lt;input&gt; --codon
+
+<span class="c1"># or</span>
+
+    clipkit &lt;input&gt; --co
+</pre></div>
+</div>
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+</div>
 <div class="section" id="sequence-type">
-<span id="id5"></span><h2>Sequence Type<a class="headerlink" href="#sequence-type" title="Permalink to this headline">¶</a></h2>
+<span id="id6"></span><h2>Sequence Type<a class="headerlink" href="#sequence-type" title="Permalink to this headline">¶</a></h2>
 <p>Specifies the type of sequences in the input file. The default
 is auto-detection of sequence type. Valid options
 include aa or nt for amino acids and nucleotides. This argument
@@ -290,7 +306,50 @@ <h2>Output<a class="headerlink" href="#id2" title="Permalink to this headline">
 </div>
 </div>
 <div class="section" id="all-options">
-<span id="id6"></span><h2>All options<a class="headerlink" href="#all-options" title="Permalink to this headline">¶</a></h2>
+<span id="id7"></span><h2>All options<a class="headerlink" href="#all-options" title="Permalink to this headline">¶</a></h2>
+<table class="docutils align-default">
+<colgroup>
+<col style="width: 30%" />
+<col style="width: 70%" />
+</colgroup>
+<thead>
+<tr class="row-odd"><th class="head"><p>Option</p></th>
+<th class="head"><p>Usage and meaning</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>-h/--help</p></td>
+<td><p>Print help message</p></td>
+</tr>
+<tr class="row-odd"><td><p>-v/--version</p></td>
+<td><p>Print software version</p></td>
+</tr>
+<tr class="row-even"><td><p>-m/--mode</p></td>
+<td><p>Specify trimming mode (default: smart-gap)</p></td>
+</tr>
+<tr class="row-odd"><td><p>-o/--output</p></td>
+<td><p>Specify output file name</p></td>
+</tr>
+<tr class="row-even"><td><p>-g/--gaps</p></td>
+<td><p>Specify gappyness threshold (between 0 and 1). <em>Default: 0.9</em></p></td>
+</tr>
+<tr class="row-odd"><td><p>-co/--codon</p></td>
+<td><p>Codon codon-based trimming. <em>Default: off</em></p></td>
+</tr>
+<tr class="row-even"><td><p>-if/--input_file_format</p></td>
+<td><p>Specify input file format*. <em>Default: auto-detect</em></p></td>
+</tr>
+<tr class="row-odd"><td><p>-of/--output_file_format</p></td>
+<td><p>Specify output file format*. <em>Default: input file type</em></p></td>
+</tr>
+<tr class="row-even"><td><p>-l/--log</p></td>
+<td><p>Create a log file. <em>Default: off</em></p></td>
+</tr>
+<tr class="row-odd"><td><p>-c/--complementary</p></td>
+<td><p>Create a complementary alignment file. <em>Default: off</em></p></td>
+</tr>
+</tbody>
+</table>
 <p>*Acceptable file formats include:
 <a class="reference external" href="https://en.wikipedia.org/wiki/FASTA_format">fasta</a>,
 <a class="reference external" href="http://meme-suite.org/doc/clustalw-format.html">clustal</a>,

diff --git a/change_log/index.html b/change_log/index.html
@@ -159,6 +159,9 @@
 <span id="id1"></span><h1>Change log<a class="headerlink" href="#change-log" title="Permalink to this headline">¶</a></h1>
 <hr class="docutils" />
 <p>Major changes to ClipKIT are summarized here.</p>
+<p><strong>2.1.2</strong>
+Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode
+being used, the whole codon will get trimmed from the alignment.</p>
 <p><strong>1.4.0</strong>
 new argument for specifying if sequences are amino acids or nucleotides</p>
 <p><strong>1.3.0</strong>

diff --git a/index.html b/index.html
@@ -252,6 +252,7 @@ <h1>Quick Start<a class="headerlink" href="#quick-start" title="Permalink to thi
 <li class="toctree-l2"><a class="reference internal" href="advanced/index.html#id2">Output</a></li>
 <li class="toctree-l2"><a class="reference internal" href="advanced/index.html#log">Log</a></li>
 <li class="toctree-l2"><a class="reference internal" href="advanced/index.html#complementary">Complementary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#codon">Codon</a></li>
 <li class="toctree-l2"><a class="reference internal" href="advanced/index.html#sequence-type">Sequence Type</a></li>
 <li class="toctree-l2"><a class="reference internal" href="advanced/index.html#all-options">All options</a></li>
 </ul>

diff --git a/objects.inv b/objects.inv