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<ul class="current">
<li class="toctree-l1 current"><a class="reference internal" href="index.html">Biopython Tutorial & Cookbook</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="chapter_introduction.html">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_quick_start.html">Quick Start – What can you do with Biopython?</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_seq_objects.html">Sequence objects</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_seq_annot.html">Sequence annotation objects</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_seqio.html">Sequence Input/Output</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Sequence alignments</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#alignment-objects">Alignment objects</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#creating-an-alignment-object-from-sequences-and-coordinates">Creating an Alignment object from sequences and coordinates</a></li>
<li class="toctree-l4"><a class="reference internal" href="#creating-an-alignment-object-from-aligned-sequences">Creating an Alignment object from aligned sequences</a></li>
<li class="toctree-l4"><a class="reference internal" href="#common-alignment-attributes">Common alignment attributes</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#slicing-and-indexing-an-alignment">Slicing and indexing an alignment</a></li>
<li class="toctree-l3"><a class="reference internal" href="#getting-information-about-the-alignment">Getting information about the alignment</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#alignment-shape">Alignment shape</a></li>
<li class="toctree-l4"><a class="reference internal" href="#comparing-alignments">Comparing alignments</a></li>
<li class="toctree-l4"><a class="reference internal" href="#finding-the-indices-of-aligned-sequences">Finding the indices of aligned sequences</a></li>
<li class="toctree-l4"><a class="reference internal" href="#counting-identities-mismatches-and-gaps">Counting identities, mismatches, and gaps</a></li>
<li class="toctree-l4"><a class="reference internal" href="#letter-frequencies">Letter frequencies</a></li>
<li class="toctree-l4"><a class="reference internal" href="#substitutions">Substitutions</a></li>
<li class="toctree-l4"><a class="reference internal" href="#alignments-as-arrays">Alignments as arrays</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#operations-on-an-alignment">Operations on an alignment</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sorting-an-alignment">Sorting an alignment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#reverse-complementing-the-alignment">Reverse-complementing the alignment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#adding-alignments">Adding alignments</a></li>
<li class="toctree-l4"><a class="reference internal" href="#mapping-a-pairwise-sequence-alignment">Mapping a pairwise sequence alignment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#mapping-a-multiple-sequence-alignment">Mapping a multiple sequence alignment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#using-from-alignments-with-same-reference">Using from_alignments_with_same_reference</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#the-alignments-class">The Alignments class</a></li>
<li class="toctree-l3"><a class="reference internal" href="#reading-and-writing-alignments">Reading and writing alignments</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#reading-alignments">Reading alignments</a></li>
<li class="toctree-l4"><a class="reference internal" href="#writing-alignments">Writing alignments</a></li>
<li class="toctree-l4"><a class="reference internal" href="#printing-alignments">Printing alignments</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#alignment-file-formats">Alignment file formats</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#aligned-fasta">Aligned FASTA</a></li>
<li class="toctree-l4"><a class="reference internal" href="#clustalw">ClustalW</a></li>
<li class="toctree-l4"><a class="reference internal" href="#stockholm">Stockholm</a></li>
<li class="toctree-l4"><a class="reference internal" href="#phylip-output-files">PHYLIP output files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#emboss">EMBOSS</a></li>
<li class="toctree-l4"><a class="reference internal" href="#gcg-multiple-sequence-format-msf">GCG Multiple Sequence Format (MSF)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#exonerate">Exonerate</a></li>
<li class="toctree-l4"><a class="reference internal" href="#nexus">NEXUS</a></li>
<li class="toctree-l4"><a class="reference internal" href="#tabular-output-from-blast-or-fasta">Tabular output from BLAST or FASTA</a></li>
<li class="toctree-l4"><a class="reference internal" href="#hh-suite-output-files">HH-suite output files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#a2m">A2M</a></li>
<li class="toctree-l4"><a class="reference internal" href="#mauve-extended-multi-fasta-xmfa-format">Mauve eXtended Multi-FastA (xmfa) format</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sequence-alignment-map-sam">Sequence Alignment/Map (SAM)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#browser-extensible-data-bed">Browser Extensible Data (BED)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#bigbed">bigBed</a></li>
<li class="toctree-l4"><a class="reference internal" href="#pattern-space-layout-psl">Pattern Space Layout (PSL)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#bigpsl">bigPsl</a></li>
<li class="toctree-l4"><a class="reference internal" href="#multiple-alignment-format-maf">Multiple Alignment Format (MAF)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#bigmaf">bigMaf</a></li>
<li class="toctree-l4"><a class="reference internal" href="#ucsc-chain-file-format">UCSC chain file format</a></li>
</ul>
</li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="chapter_pairwise.html">Pairwise sequence alignment</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_msa.html">Multiple Sequence Alignment objects</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_pairwise2.html">Pairwise alignments using pairwise2</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_blast.html">BLAST (new)</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_blast.html#blast-old">BLAST (old)</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_searchio.html">BLAST and other sequence search tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_entrez.html">Accessing NCBI’s Entrez databases</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_uniprot.html">Swiss-Prot and ExPASy</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_pdb.html">Going 3D: The PDB module</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_popgen.html">Bio.PopGen: Population genetics</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_phylo.html">Phylogenetics with Bio.Phylo</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_motifs.html">Sequence motif analysis using Bio.motifs</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_cluster.html">Cluster analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_graphics.html">Graphics including GenomeDiagram</a></li>
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<li class="toctree-l2"><a class="reference internal" href="chapter_testing.html">The Biopython testing framework</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_contributing.html">Where to go from here – contributing to Biopython</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_appendix.html">Appendix: Useful stuff about Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_bibliography.html">Bibliography</a></li>
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<section id="sequence-alignments">
<span id="chapter-align"></span><h1>Sequence alignments<a class="headerlink" href="#sequence-alignments" title="Link to this heading"></a></h1>
<p>Sequence alignments are a collection of two or more sequences that have
been aligned to each other – usually with the insertion of gaps, and the
addition of leading or trailing gaps – such that all the sequence
strings are the same length.</p>
<p>Alignments may extend over the full length of each sequence, or may be
limited to a subsection of each sequence. In Biopython, all sequence
alignments are represented by an <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object, described in
section <a class="reference internal" href="#sec-alignmentobject"><span class="std std-ref">Alignment objects</span></a>. <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> objects can be
obtained by parsing the output of alignment software such as Clustal or
BLAT (described in section <a class="reference internal" href="#sec-alignmentparsers"><span class="std std-ref">Reading and writing alignments</span></a>. or by using
Biopython’s pairwise sequence aligner, which can align two sequences to
each other (described in
Chapter <a class="reference internal" href="chapter_pairwise.html#chapter-pairwise"><span class="std std-ref">Pairwise sequence alignment</span></a>).</p>
<p>See Chapter <a class="reference internal" href="chapter_msa.html#chapter-msa"><span class="std std-ref">Multiple Sequence Alignment objects</span></a> for a description of the
older <code class="docutils literal notranslate"><span class="pre">MultipleSeqAlignment</span></code> class and the parsers in <code class="docutils literal notranslate"><span class="pre">Bio.AlignIO</span></code>
that parse the output of sequence alignment software, generating
<code class="docutils literal notranslate"><span class="pre">MultipleSeqAlignment</span></code> objects.</p>
<section id="alignment-objects">
<span id="sec-alignmentobject"></span><h2>Alignment objects<a class="headerlink" href="#alignment-objects" title="Link to this heading"></a></h2>
<p>The <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> class is defined in <code class="docutils literal notranslate"><span class="pre">Bio.Align</span></code>. Usually you would
get an <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object by parsing the output of alignment programs
(section <a class="reference internal" href="#sec-alignmentparsers"><span class="std std-ref">Reading and writing alignments</span></a>) or by running Biopython’s
pairwise aligner (Chapter <a class="reference internal" href="chapter_pairwise.html#chapter-pairwise"><span class="std std-ref">Pairwise sequence alignment</span></a>).
For the benefit of this section, however, we will create an
<code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object from scratch.</p>
<section id="creating-an-alignment-object-from-sequences-and-coordinates">
<span id="subsec-align-sequences-coordinates"></span><h3>Creating an Alignment object from sequences and coordinates<a class="headerlink" href="#creating-an-alignment-object-from-sequences-and-coordinates" title="Link to this heading"></a></h3>
<p>Suppose you have three sequences:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">seqA</span> <span class="o">=</span> <span class="s2">"CCGGTTTTT"</span>
<span class="gp">>>> </span><span class="n">seqB</span> <span class="o">=</span> <span class="s2">"AGTTTAA"</span>
<span class="gp">>>> </span><span class="n">seqC</span> <span class="o">=</span> <span class="s2">"AGGTTT"</span>
<span class="gp">>>> </span><span class="n">sequences</span> <span class="o">=</span> <span class="p">[</span><span class="n">seqA</span><span class="p">,</span> <span class="n">seqB</span><span class="p">,</span> <span class="n">seqC</span><span class="p">]</span>
</pre></div>
</div>
<p>To create an <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object, we also need the coordinates that
define how the sequences are aligned to each other. We use a NumPy array
for that:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="gp">>>> </span><span class="n">coordinates</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">7</span><span class="p">,</span> <span class="mi">9</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">5</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="mi">6</span><span class="p">]])</span>
</pre></div>
</div>
<p>These coordinates define the alignment for the following sequence
segments:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">SeqA[1:3]</span></code>, <code class="docutils literal notranslate"><span class="pre">SeqB[0:2]</span></code>, and <code class="docutils literal notranslate"><span class="pre">SeqC[0:2]</span></code> are aligned to each
other;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SeqA[3:4]</span></code> and <code class="docutils literal notranslate"><span class="pre">SeqC[2:3]</span></code> are aligned to each other, with a gap
of one nucleotide in <code class="docutils literal notranslate"><span class="pre">seqB</span></code>;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SeqA[4:7]</span></code>, <code class="docutils literal notranslate"><span class="pre">SeqB[2:5]</span></code>, and <code class="docutils literal notranslate"><span class="pre">SeqC[3:6]</span></code> are aligned to each
other;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SeqA[7:9]</span></code> is not aligned to <code class="docutils literal notranslate"><span class="pre">seqB</span></code> or <code class="docutils literal notranslate"><span class="pre">seqC</span></code>.</p></li>
</ul>
<p>Note that the alignment does not include the first nucleotide of
<code class="docutils literal notranslate"><span class="pre">seqA</span></code> and last two nucleotides of <code class="docutils literal notranslate"><span class="pre">seqB</span></code>.</p>
<p>Now we can create the <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Align</span><span class="w"> </span><span class="kn">import</span> <span class="n">Alignment</span>
<span class="gp">>>> </span><span class="n">alignment</span> <span class="o">=</span> <span class="n">Alignment</span><span class="p">(</span><span class="n">sequences</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">alignment</span>
<span class="go"><Alignment object (3 rows x 8 columns) at ...></span>
</pre></div>
</div>
<p>The alignment object has an attribute <code class="docutils literal notranslate"><span class="pre">sequences</span></code> pointing to the
sequences included in this alignment:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">sequences</span>
<span class="go">['CCGGTTTTT', 'AGTTTAA', 'AGGTTT']</span>
</pre></div>
</div>
<p>and an attribute <code class="docutils literal notranslate"><span class="pre">coordinates</span></code> with the alignment coordinates:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">coordinates</span>
<span class="go">array([[1, 3, 4, 7, 9],</span>
<span class="go"> [0, 2, 2, 5, 5],</span>
<span class="go"> [0, 2, 3, 6, 6]])</span>
</pre></div>
</div>
<p>Print the <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object to show the alignment explicitly:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
<span class="go"> 1 CGGTTTTT 9</span>
<span class="go"> 0 AG-TTT-- 5</span>
<span class="go"> 0 AGGTTT-- 6</span>
</pre></div>
</div>
<p>with the starting and end coordinate for each sequence are shown to the
left and right, respectively, of the alignment.</p>
</section>
<section id="creating-an-alignment-object-from-aligned-sequences">
<span id="subsec-align-parse-printed-alignment"></span><h3>Creating an Alignment object from aligned sequences<a class="headerlink" href="#creating-an-alignment-object-from-aligned-sequences" title="Link to this heading"></a></h3>
<p>If you start out with the aligned sequences, with dashes representing
gaps, then you can calculate the coordinates using the
<code class="docutils literal notranslate"><span class="pre">parse_printed_alignment</span></code> class method. This method is primarily employed in
Biopython’s alignment parsers (see
Section <a class="reference internal" href="#sec-alignmentparsers"><span class="std std-ref">Reading and writing alignments</span></a>), but it may be useful for other
purposes. For example, you can construct the <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object from
aligned sequences as follows:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">lines</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"CGGTTTTT"</span><span class="p">,</span> <span class="s2">"AG-TTT--"</span><span class="p">,</span> <span class="s2">"AGGTTT--"</span><span class="p">]</span>
<span class="gp">>>> </span><span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span>
<span class="gp">... </span> <span class="nb">print</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
<span class="gp">...</span>
<span class="go">CGGTTTTT</span>
<span class="go">AG-TTT--</span>
<span class="go">AGGTTT--</span>
<span class="gp">>>> </span><span class="n">lines</span> <span class="o">=</span> <span class="p">[</span><span class="n">line</span><span class="o">.</span><span class="n">encode</span><span class="p">()</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">]</span> <span class="c1"># convert to bytes</span>
<span class="gp">>>> </span><span class="n">lines</span>
<span class="go">[b'CGGTTTTT', b'AG-TTT--', b'AGGTTT--']</span>
<span class="gp">>>> </span><span class="n">sequences</span><span class="p">,</span> <span class="n">coordinates</span> <span class="o">=</span> <span class="n">Alignment</span><span class="o">.</span><span class="n">parse_printed_alignment</span><span class="p">(</span><span class="n">lines</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">sequences</span>
<span class="go">[b'CGGTTTTT', b'AGTTT', b'AGGTTT']</span>
<span class="gp">>>> </span><span class="n">sequences</span> <span class="o">=</span> <span class="p">[</span><span class="n">sequence</span><span class="o">.</span><span class="n">decode</span><span class="p">()</span> <span class="k">for</span> <span class="n">sequence</span> <span class="ow">in</span> <span class="n">sequences</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">sequences</span>
<span class="go">['CGGTTTTT', 'AGTTT', 'AGGTTT']</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">coordinates</span><span class="p">)</span>
<span class="go">[[0 2 3 6 8]</span>
<span class="go"> [0 2 2 5 5]</span>
<span class="go"> [0 2 3 6 6]]</span>
</pre></div>
</div>
<p>The initial <code class="docutils literal notranslate"><span class="pre">G</span></code> nucleotide of <code class="docutils literal notranslate"><span class="pre">seqA</span></code> and the final <code class="docutils literal notranslate"><span class="pre">CC</span></code>
nucleotides of <code class="docutils literal notranslate"><span class="pre">seqB</span></code> were not included in the alignment and is
therefore missing here. But this is easy to fix:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Seq</span><span class="w"> </span><span class="kn">import</span> <span class="n">Seq</span>
<span class="gp">>>> </span><span class="n">sequences</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"C"</span> <span class="o">+</span> <span class="n">sequences</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">sequences</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">sequences</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s2">"AA"</span>
<span class="gp">>>> </span><span class="n">sequences</span>
<span class="go">['CCGGTTTTT', 'AGTTTAA', 'AGGTTT']</span>
<span class="gp">>>> </span><span class="n">coordinates</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="p">:]</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">coordinates</span><span class="p">)</span>
<span class="go">[[1 3 4 7 9]</span>
<span class="go"> [0 2 2 5 5]</span>
<span class="go"> [0 2 3 6 6]]</span>
</pre></div>
</div>
<p>Now we can create the <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span> <span class="o">=</span> <span class="n">Alignment</span><span class="p">(</span><span class="n">sequences</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
<span class="go"> 1 CGGTTTTT 9</span>
<span class="go"> 0 AG-TTT-- 5</span>
<span class="go"> 0 AGGTTT-- 6</span>
</pre></div>
</div>
<p>which identical to the <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object created above in
section <a class="reference internal" href="#subsec-align-sequences-coordinates"><span class="std std-ref">Creating an Alignment object from sequences and coordinates</span></a>.</p>
<p>By default, the <code class="docutils literal notranslate"><span class="pre">coordinates</span></code> argument to the <code class="docutils literal notranslate"><span class="pre">Alignment</span></code>
initializer is <code class="docutils literal notranslate"><span class="pre">None</span></code>, which assumes that there are no gaps in the
alignment. All sequences in an ungapped alignment must have the same
length. If the <code class="docutils literal notranslate"><span class="pre">coordinates</span></code> argument is <code class="docutils literal notranslate"><span class="pre">None</span></code>, then the
initializer will fill in the <code class="docutils literal notranslate"><span class="pre">coordinates</span></code> attribute of the
<code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object for you:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">ungapped_alignment</span> <span class="o">=</span> <span class="n">Alignment</span><span class="p">([</span><span class="s2">"ACGTACGT"</span><span class="p">,</span> <span class="s2">"AAGTACGT"</span><span class="p">,</span> <span class="s2">"ACGTACCT"</span><span class="p">])</span>
<span class="gp">>>> </span><span class="n">ungapped_alignment</span>
<span class="go"><Alignment object (3 rows x 8 columns) at ...></span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">ungapped_alignment</span><span class="o">.</span><span class="n">coordinates</span><span class="p">)</span>
<span class="go">[[0 8]</span>
<span class="go"> [0 8]</span>
<span class="go"> [0 8]]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">ungapped_alignment</span><span class="p">)</span>
<span class="go"> 0 ACGTACGT 8</span>
<span class="go"> 0 AAGTACGT 8</span>
<span class="go"> 0 ACGTACCT 8</span>
</pre></div>
</div>
</section>
<section id="common-alignment-attributes">
<span id="subsec-align-common-attributes"></span><h3>Common alignment attributes<a class="headerlink" href="#common-alignment-attributes" title="Link to this heading"></a></h3>
<p>The following attributes are commonly found on <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> objects:</p>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">sequences</span></code>: This is a list of the sequences aligned to each other.
Depending on how the alignment was created, the sequences can have
the following types:</p>
<ul class="simple">
<li><p>plain Python string;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Seq</span></code>;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">MutableSeq</span></code>;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code>;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">bytes</span></code>;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">bytearray</span></code>;</p></li>
<li><p>NumPy array with data type <code class="docutils literal notranslate"><span class="pre">numpy.int32</span></code>;</p></li>
<li><p>any other object with a contiguous buffer of format <code class="docutils literal notranslate"><span class="pre">"c"</span></code>,
<code class="docutils literal notranslate"><span class="pre">"B"</span></code>, <code class="docutils literal notranslate"><span class="pre">"i"</span></code>, or <code class="docutils literal notranslate"><span class="pre">"I"</span></code>;</p></li>
<li><p>lists or tuples of objects defined in the <code class="docutils literal notranslate"><span class="pre">alphabet</span></code> attribute
of the <code class="docutils literal notranslate"><span class="pre">PairwiseAligner</span></code> object that created the alignment (see
section <a class="reference internal" href="chapter_pairwise.html#sec-generalized-pairwise"><span class="std std-ref">Generalized pairwise alignments</span></a>).</p></li>
</ul>
<p>For pairwise alignments (meaning an alignment of two sequences), the
properties <code class="docutils literal notranslate"><span class="pre">target</span></code> and <code class="docutils literal notranslate"><span class="pre">query</span></code> are aliases for <code class="docutils literal notranslate"><span class="pre">sequences[0]</span></code>
and <code class="docutils literal notranslate"><span class="pre">sequences[1]</span></code>, respectively.</p>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">coordinates</span></code>: A NumPy array of integers storing the sequence
indices defining how the sequences are aligned to each other;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">score</span></code>: The alignment score, as found by the parser in the
alignment file, or as calculated by the <code class="docutils literal notranslate"><span class="pre">PairwiseAligner</span></code> (see
section <a class="reference internal" href="chapter_pairwise.html#sec-pairwise-basic"><span class="std std-ref">Pairwise sequence alignments using the pairwise aligner</span></a>);</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">annotations</span></code>: A dictionary storing most other annotations
associated with the alignment;</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">column_annotations</span></code>: A dictionary storing annotations that extend
along the alignment and have the same length as the alignment, such
as a consensus sequence (see
section <a class="reference internal" href="#subsec-align-clustal"><span class="std std-ref">ClustalW</span></a> for an example).</p></li>
</ul>
<p>An <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object created by the parser in <code class="docutils literal notranslate"><span class="pre">Bio.Align</span></code> may have
additional attributes, depending on the alignment file format from which
the alignment was read.</p>
</section>
</section>
<section id="slicing-and-indexing-an-alignment">
<span id="subsec-slicing-indexing-alignment"></span><h2>Slicing and indexing an alignment<a class="headerlink" href="#slicing-and-indexing-an-alignment" title="Link to this heading"></a></h2>
<p>Slices of the form <code class="docutils literal notranslate"><span class="pre">alignment[k,</span> <span class="pre">i:j]</span></code>, where <code class="docutils literal notranslate"><span class="pre">k</span></code> is an integer and
<code class="docutils literal notranslate"><span class="pre">i</span></code> and <code class="docutils literal notranslate"><span class="pre">j</span></code> are integers or are absent, return a string showing the
aligned sequence (including gaps) for the target (if <code class="docutils literal notranslate"><span class="pre">k=0</span></code>) or the
query (if <code class="docutils literal notranslate"><span class="pre">k=1</span></code>) that includes only the columns <code class="docutils literal notranslate"><span class="pre">i</span></code> through <code class="docutils literal notranslate"><span class="pre">j</span></code> in
the printed alignment.</p>
<p>To illustrate this, in the following example the printed alignment has 8
columns:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
<span class="go"> 1 CGGTTTTT 9</span>
<span class="go"> 0 AG-TTT-- 5</span>
<span class="go"> 0 AGGTTT-- 6</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">length</span>
<span class="go">8</span>
</pre></div>
</div>
<p>To get the aligned sequence strings individually, use</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="go">'CGGTTTTT'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="go">'AG-TTT--'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="go">'AGGTTT--'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="p">:]</span>
<span class="go">'CGGTTTTT'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="p">:]</span>
<span class="go">'AG-TTT--'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="go">'GGTTTT'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="go">'G-TTT-'</span>
</pre></div>
</div>
<p>Columns to be included can also be selected using an iterable over
integers:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">)]</span>
<span class="go">'GGT'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span>
<span class="go">'A-T'</span>
</pre></div>
</div>
<p>To get the letter at position <code class="docutils literal notranslate"><span class="pre">[i,</span> <span class="pre">j]</span></code> of the printed alignment, use
<code class="docutils literal notranslate"><span class="pre">alignment[i,</span> <span class="pre">j]</span></code>; this will return <code class="docutils literal notranslate"><span class="pre">"-"</span></code> if a gap is found at that
position:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="go">'G'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">6</span><span class="p">]</span>
<span class="go">'-'</span>
</pre></div>
</div>
<p>To get specific columns in the alignment, use</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span>
<span class="go">'CAA'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]</span>
<span class="go">'GGG'</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">]</span>
<span class="go">'G-G'</span>
</pre></div>
</div>
<p>Slices of the form <code class="docutils literal notranslate"><span class="pre">alignment[i:j:k]</span></code> return a new <code class="docutils literal notranslate"><span class="pre">Alignment</span></code>
object including only sequences <code class="docutils literal notranslate"><span class="pre">[i:j:k]</span></code> of the alignment:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
<span class="go"><Alignment object (2 rows x 6 columns) at ...></span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
<span class="go">target 0 AG-TTT 5</span>
<span class="go"> 0 ||-||| 6</span>
<span class="go">query 0 AGGTTT 6</span>
</pre></div>
</div>
<p>Slices of the form <code class="docutils literal notranslate"><span class="pre">alignment[:,</span> <span class="pre">i:j]</span></code>, where <code class="docutils literal notranslate"><span class="pre">i</span></code> and <code class="docutils literal notranslate"><span class="pre">j</span></code> are
integers or are absent, return a new <code class="docutils literal notranslate"><span class="pre">Alignment</span></code> object that includes
only the columns <code class="docutils literal notranslate"><span class="pre">i</span></code> through <code class="docutils literal notranslate"><span class="pre">j</span></code> in the printed alignment.</p>
<p>Extracting the first 4 columns for the example alignment above gives:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[:,</span> <span class="p">:</span><span class="mi">4</span><span class="p">]</span>
<span class="go"><Alignment object (3 rows x 4 columns) at ...></span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">[:,</span> <span class="p">:</span><span class="mi">4</span><span class="p">])</span>
<span class="go"> 1 CGGT 5</span>
<span class="go"> 0 AG-T 3</span>
<span class="go"> 0 AGGT 4</span>
</pre></div>
</div>
<p>Similarly, extracting the last 6 columns gives:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="p">[:,</span> <span class="o">-</span><span class="mi">6</span><span class="p">:]</span>
<span class="go"><Alignment object (3 rows x 6 columns) at ...></span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">[:,</span> <span class="o">-</span><span class="mi">6</span><span class="p">:])</span>
<span class="go"> 3 GTTTTT 9</span>
<span class="go"> 2 -TTT-- 5</span>
<span class="go"> 2 GTTT-- 6</span>
</pre></div>
</div>
<p>The column index can also be an iterable of integers:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">[:,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">0</span><span class="p">)])</span>
<span class="go"> 0 GTC 3</span>
<span class="go"> 0 GTA 3</span>
<span class="go"> 0 GTA 3</span>
</pre></div>
</div>
<p>Calling <code class="docutils literal notranslate"><span class="pre">alignment[:,</span> <span class="pre">:]</span></code> returns a copy of the alignment.</p>
</section>
<section id="getting-information-about-the-alignment">
<h2>Getting information about the alignment<a class="headerlink" href="#getting-information-about-the-alignment" title="Link to this heading"></a></h2>
<section id="alignment-shape">
<h3>Alignment shape<a class="headerlink" href="#alignment-shape" title="Link to this heading"></a></h3>
<p>The number of aligned sequences is returned by <code class="docutils literal notranslate"><span class="pre">len(alignment)</span></code>:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
<span class="go">3</span>
</pre></div>
</div>
<p>The alignment length is defined as the number of columns in the
alignment as printed. This is equal to the sum of the number of matches,
number of mismatches, and the total length of gaps in each sequence:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">length</span>
<span class="go">8</span>
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">shape</span></code> property returns a tuple consisting of the length of the
alignment and the number of columns in the alignment as printed:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">shape</span>
<span class="go">(3, 8)</span>
</pre></div>
</div>
</section>
<section id="comparing-alignments">
<h3>Comparing alignments<a class="headerlink" href="#comparing-alignments" title="Link to this heading"></a></h3>
<p>Two alignments are equal to each other (meaning that
<code class="docutils literal notranslate"><span class="pre">alignment1</span> <span class="pre">==</span> <span class="pre">alignment2</span></code> evaluates to <code class="docutils literal notranslate"><span class="pre">True</span></code>) if each of the
sequences in <code class="docutils literal notranslate"><span class="pre">alignment1.sequences</span></code> and <code class="docutils literal notranslate"><span class="pre">alignment2.sequences</span></code> are
equal to each other, and <code class="docutils literal notranslate"><span class="pre">alignment1.coordinates</span></code> and
<code class="docutils literal notranslate"><span class="pre">alignment2.coordinates</span></code> contain the same coordinates. If either of
these conditions is not fulfilled, then <code class="docutils literal notranslate"><span class="pre">alignment1</span> <span class="pre">==</span> <span class="pre">alignment2</span></code>
evaluates to <code class="docutils literal notranslate"><span class="pre">False</span></code>. Inequality of two alignments (e.g.,
<code class="docutils literal notranslate"><span class="pre">alignment1</span> <span class="pre"><</span> <span class="pre">alignment2</span></code>) is established by first comparing
<code class="docutils literal notranslate"><span class="pre">alignment1.sequences</span></code> and <code class="docutils literal notranslate"><span class="pre">alignment2.sequences</span></code>, and if they are
equal, by comparing <code class="docutils literal notranslate"><span class="pre">alignment1.coordinates</span></code> to
<code class="docutils literal notranslate"><span class="pre">alignment2.coordinates</span></code>.</p>
</section>
<section id="finding-the-indices-of-aligned-sequences">
<h3>Finding the indices of aligned sequences<a class="headerlink" href="#finding-the-indices-of-aligned-sequences" title="Link to this heading"></a></h3>
<p>For pairwise alignments, the <code class="docutils literal notranslate"><span class="pre">aligned</span></code> property of an alignment
returns the start and end indices of subsequences in the target and
query sequence that were aligned to each other. If the alignment between
target (t) and query (q) consists of <span class="math notranslate nohighlight">\(N\)</span> chunks, you get two
tuples of length <span class="math notranslate nohighlight">\(N\)</span>:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>(((t_start1, t_end1), (t_start2, t_end2), ..., (t_startN, t_endN)),
((q_start1, q_end1), (q_start2, q_end2), ..., (q_startN, q_endN)))
</pre></div>
</div>
<p>For example,</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">pairwise_alignment</span> <span class="o">=</span> <span class="n">alignment</span><span class="p">[:</span><span class="mi">2</span><span class="p">,</span> <span class="p">:]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment</span><span class="p">)</span>
<span class="go">target 1 CGGTTTTT 9</span>
<span class="go"> 0 .|-|||-- 8</span>
<span class="go">query 0 AG-TTT-- 5</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">aligned</span><span class="p">)</span>
<span class="go">[[[1 3]</span>
<span class="go"> [4 7]]</span>
<span class="go"> [[0 2]</span>
<span class="go"> [2 5]]]</span>
</pre></div>
</div>
<p>Note that different alignments may have the same subsequences aligned to
each other. In particular, this may occur if alignments differ from each
other in terms of their gap placement only:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">pairwise_alignment1</span> <span class="o">=</span> <span class="n">Alignment</span><span class="p">([</span><span class="s2">"AAACAAA"</span><span class="p">,</span> <span class="s2">"AAAGAAA"</span><span class="p">],</span>
<span class="gp">... </span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">7</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">7</span><span class="p">]]))</span> <span class="c1"># fmt: skip</span>
<span class="gp">...</span>
<span class="gp">>>> </span><span class="n">pairwise_alignment2</span> <span class="o">=</span> <span class="n">Alignment</span><span class="p">([</span><span class="s2">"AAACAAA"</span><span class="p">,</span> <span class="s2">"AAAGAAA"</span><span class="p">],</span>
<span class="gp">... </span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">7</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">7</span><span class="p">]]))</span> <span class="c1"># fmt: skip</span>
<span class="gp">...</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment1</span><span class="p">)</span>
<span class="go">target 0 AAAC-AAA 7</span>
<span class="go"> 0 |||--||| 8</span>
<span class="go">query 0 AAA-GAAA 7</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment2</span><span class="p">)</span>
<span class="go">target 0 AAA-CAAA 7</span>
<span class="go"> 0 |||--||| 8</span>
<span class="go">query 0 AAAG-AAA 7</span>
<span class="gp">>>> </span><span class="n">pairwise_alignment1</span><span class="o">.</span><span class="n">aligned</span>
<span class="go">array([[[0, 3],</span>
<span class="go"> [4, 7]],</span>
<span class="go"> [[0, 3],</span>
<span class="go"> [4, 7]]])</span>
<span class="gp">>>> </span><span class="n">pairwise_alignment2</span><span class="o">.</span><span class="n">aligned</span>
<span class="go">array([[[0, 3],</span>
<span class="go"> [4, 7]],</span>
<span class="go"> [[0, 3],</span>
<span class="go"> [4, 7]]])</span>
</pre></div>
</div>
<p>The property <code class="docutils literal notranslate"><span class="pre">indices</span></code> returns a 2D NumPy array with the sequence
index of each letter in the alignment, with gaps indicated by -1:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
<span class="go"> 1 CGGTTTTT 9</span>
<span class="go"> 0 AG-TTT-- 5</span>
<span class="go"> 0 AGGTTT-- 6</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">indices</span>
<span class="go">array([[ 1, 2, 3, 4, 5, 6, 7, 8],</span>
<span class="go"> [ 0, 1, -1, 2, 3, 4, -1, -1],</span>
<span class="go"> [ 0, 1, 2, 3, 4, 5, -1, -1]])</span>
</pre></div>
</div>
<p>The property <code class="docutils literal notranslate"><span class="pre">inverse_indices</span></code> returns a list of 1D NumPy arrays, one
for each of the aligned sequences, with the column index in the
alignment for each letter in the sequence. Letters not included in the
alignment are indicated by -1:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">sequences</span>
<span class="go">['CCGGTTTTT', 'AGTTTAA', 'AGGTTT']</span>
<span class="gp">>>> </span><span class="n">alignment</span><span class="o">.</span><span class="n">inverse_indices</span>
<span class="go">[array([-1, 0, 1, 2, 3, 4, 5, 6, 7]),</span>
<span class="go"> array([ 0, 1, 3, 4, 5, -1, -1]),</span>
<span class="go"> array([0, 1, 2, 3, 4, 5])]</span>
</pre></div>
</div>
</section>
<section id="counting-identities-mismatches-and-gaps">
<span id="paragraph-alignment-counts"></span><h3>Counting identities, mismatches, and gaps<a class="headerlink" href="#counting-identities-mismatches-and-gaps" title="Link to this heading"></a></h3>
<p>The <code class="docutils literal notranslate"><span class="pre">counts</span></code> method counts the number of identities, mismatches, aligned
letters, and gaps (insertions and deletions) in an alignment. The return
value is an <code class="docutils literal notranslate"><span class="pre">AlignmentCounts</span></code> object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment</span><span class="p">)</span>
<span class="go">target 1 CGGTTTTT 9</span>
<span class="go"> 0 .|-|||-- 8</span>
<span class="go">query 0 AG-TTT-- 5</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">counts</span>
<span class="go"><AlignmentCounts object (5 aligned letters; 4 identities; 1 mismatches; 3 gaps) at ...></span>
</pre></div>
</div>
<p>You can print the alignment to get detailed information about the alignment
statistics:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="p">)</span>
<span class="go">AlignmentCounts object with</span>
<span class="go"> aligned = 5:</span>
<span class="go"> identities = 4,</span>
<span class="go"> mismatches = 1.</span>
<span class="go"> gaps = 3:</span>
<span class="go"> left_gaps = 0:</span>
<span class="go"> left_insertions = 0:</span>
<span class="go"> open_left_insertions = 0,</span>
<span class="go"> extend_left_insertions = 0;</span>
<span class="go"> left_deletions = 0:</span>
<span class="go"> open_left_deletions = 0,</span>
<span class="go"> extend_left_deletions = 0;</span>
<span class="go"> internal_gaps = 1:</span>
<span class="go"> internal_insertions = 0:</span>
<span class="go"> open_internal_insertions = 0,</span>
<span class="go"> extend_internal_insertions = 0;</span>
<span class="go"> internal_deletions = 1:</span>
<span class="go"> open_internal_deletions = 1,</span>
<span class="go"> extend_internal_deletions = 0;</span>
<span class="go"> right_gaps = 2:</span>
<span class="go"> right_insertions = 0:</span>
<span class="go"> open_right_insertions = 0,</span>
<span class="go"> extend_right_insertions = 0;</span>
<span class="go"> right_deletions = 2:</span>
<span class="go"> open_right_deletions = 1,</span>
<span class="go"> extend_right_deletions = 1.</span>
</pre></div>
</div>
<p>These statistics can also be obtained as properties of the <code class="docutils literal notranslate"><span class="pre">counts</span></code> object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">aligned</span>
<span class="go">5</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span>
<span class="go">4</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span>
<span class="go">1</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">gaps</span>
<span class="go">3</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">insertions</span>
<span class="go">0</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">deletions</span>
<span class="go">3</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">internal_deletions</span>
<span class="go">1</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">right_deletions</span>
<span class="go">2</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">extend_right_deletions</span>
<span class="go">1</span>
</pre></div>
</div>
<p>Use a single character as the argument to <code class="docutils literal notranslate"><span class="pre">.counts</span></code> to specify a wildcard
character, which is ignored when counting identities, positives, and mismatches
(e.g. <code class="docutils literal notranslate"><span class="pre">"?"</span></code> or <code class="docutils literal notranslate"><span class="pre">"N"</span></code> are commonly used as wildcard characters):</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">sequences</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"CCGGT?TTT"</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment</span><span class="p">)</span>
<span class="go">target 1 CGGT?TTT 9</span>
<span class="go"> 0 .|-|.|-- 8</span>
<span class="go">query 0 AG-TTT-- 5</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span>
<span class="go">3</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span>
<span class="go">2</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">(</span><span class="s2">"?"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span>
<span class="go">3</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span>
<span class="go">1</span>
</pre></div>
</div>
<p>Here, the alignment between <code class="docutils literal notranslate"><span class="pre">?</span></code> and <code class="docutils literal notranslate"><span class="pre">T</span></code> is not counted as a mismatch, as
<code class="docutils literal notranslate"><span class="pre">?</span></code> is the wildcard character.</p>
<p>Use a substitution matrix (see section <a class="reference internal" href="chapter_pairwise.html#sec-substitution-matrices"><span class="std std-ref">Substitution matrices</span></a>) as the
argument to also calculate the number of positive matches, and the total
substitution score:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">protein_alignment</span> <span class="o">=</span> <span class="n">Alignment</span><span class="p">(</span>
<span class="gp">... </span> <span class="p">[</span><span class="s2">"EPQSDPSVEPPLSQETFSDLWKLLPE"</span><span class="p">,</span> <span class="s2">"EPSSETGMDPPLSQETFEDLWSLLPD"</span><span class="p">]</span>
<span class="gp">... </span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">protein_alignment</span><span class="p">)</span>
<span class="go">target 0 EPQSDPSVEPPLSQETFSDLWKLLPE 26</span>
<span class="go"> 0 ||.|.....||||||||.|||.|||. 26</span>
<span class="go">query 0 EPSSETGMDPPLSQETFEDLWSLLPD 26</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">protein_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">()</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span><span class="p">)</span>
<span class="go">17</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span><span class="p">)</span>
<span class="go">9</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">positives</span><span class="p">)</span>
<span class="go">None</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">substitution_score</span><span class="p">)</span>
<span class="go">None</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Align</span><span class="w"> </span><span class="kn">import</span> <span class="n">substitution_matrices</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">blosum62</span> <span class="o">=</span> <span class="n">substitution_matrices</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"BLOSUM62"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">protein_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">(</span><span class="n">blosum62</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span><span class="p">)</span>
<span class="go">17</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span><span class="p">)</span>
<span class="go">9</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">positives</span><span class="p">)</span>
<span class="go">21</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">substitution_score</span><span class="p">)</span>
<span class="go">101.0</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">blosum45</span> <span class="o">=</span> <span class="n">substitution_matrices</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"BLOSUM45"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">protein_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">(</span><span class="n">blosum45</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span><span class="p">)</span>
<span class="go">17</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span><span class="p">)</span>
<span class="go">9</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">positives</span><span class="p">)</span>
<span class="go">21</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">substitution_score</span><span class="p">)</span>
<span class="go">122.0</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">blosum90</span> <span class="o">=</span> <span class="n">substitution_matrices</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"BLOSUM90"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">protein_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">(</span><span class="n">blosum90</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span><span class="p">)</span>
<span class="go">17</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span><span class="p">)</span>
<span class="go">9</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">positives</span><span class="p">)</span>
<span class="go">20</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">substitution_score</span><span class="p">)</span>
<span class="go">109.0</span>
</pre></div>
</div>
<p>Use a pairwise aligner object (see Chapter <a class="reference internal" href="chapter_pairwise.html#chapter-pairwise"><span class="std std-ref">Pairwise sequence alignment</span></a>) to
also calculate the gap score and the alignment score:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Align</span><span class="w"> </span><span class="kn">import</span> <span class="n">PairwiseAligner</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">sequences</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"CCGGTTTTT"</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">pairwise_alignment</span><span class="p">)</span>
<span class="go">target 1 CGGTTTTT 9</span>
<span class="go"> 0 .|-|||-- 8</span>
<span class="go">query 0 AG-TTT-- 5</span>
<span class="gp">>>> </span><span class="n">aligner</span> <span class="o">=</span> <span class="n">PairwiseAligner</span><span class="p">(</span><span class="s2">"blastn"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">pairwise_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">(</span><span class="n">aligner</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span>
<span class="go"><AlignmentCounts object (score = -11.0; substitution score = 5.0; gap score = -16.0; 5 aligned letters; 4 identities; 1 mismatches; 4 positives; 3 gaps) at ...></span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="p">)</span>
<span class="go">AlignmentCounts object with</span>
<span class="go"> score = -11.0:</span>
<span class="go"> substitution_score = 5.0,</span>
<span class="go"> gap_score = -16.0.</span>
<span class="go"> aligned = 5:</span>
<span class="go"> identities = 4,</span>
<span class="go"> positives = 4,</span>
<span class="go"> mismatches = 1.</span>
<span class="go"> gaps = 3:</span>
<span class="go"> left_gaps = 0:</span>
<span class="go"> left_insertions = 0:</span>
<span class="go"> open_left_insertions = 0,</span>
<span class="go"> extend_left_insertions = 0;</span>
<span class="go"> left_deletions = 0:</span>
<span class="go"> open_left_deletions = 0,</span>
<span class="go"> extend_left_deletions = 0;</span>
<span class="go"> internal_gaps = 1:</span>
<span class="go"> internal_insertions = 0:</span>
<span class="go"> open_internal_insertions = 0,</span>
<span class="go"> extend_internal_insertions = 0;</span>
<span class="go"> internal_deletions = 1:</span>
<span class="go"> open_internal_deletions = 1,</span>
<span class="go"> extend_internal_deletions = 0;</span>
<span class="go"> right_gaps = 2:</span>
<span class="go"> right_insertions = 0:</span>
<span class="go"> open_right_insertions = 0,</span>
<span class="go"> extend_right_insertions = 0;</span>
<span class="go"> right_deletions = 2:</span>
<span class="go"> open_right_deletions = 1,</span>
<span class="go"> extend_right_deletions = 1.</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">aligner</span> <span class="o">=</span> <span class="n">PairwiseAligner</span><span class="p">(</span><span class="s2">"blastp"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">protein_alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">(</span><span class="n">aligner</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">counts</span>
<span class="go"><AlignmentCounts object (score = 101.0; substitution score = 101.0; gap score = 0.0; 26 aligned letters; 17 identities; 9 mismatches; 21 positives; 0 gaps) at ...></span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="p">)</span>
<span class="go">AlignmentCounts object with</span>
<span class="go"> score = 101.0:</span>
<span class="go"> substitution_score = 101.0,</span>
<span class="go"> gap_score = 0.0.</span>
<span class="go"> aligned = 26:</span>
<span class="go"> identities = 17,</span>
<span class="go"> positives = 21,</span>
<span class="go"> mismatches = 9.</span>
<span class="go"> gaps = 0:</span>
<span class="go"> left_gaps = 0:</span>
<span class="go"> left_insertions = 0:</span>
<span class="go"> open_left_insertions = 0,</span>
<span class="go"> extend_left_insertions = 0;</span>
<span class="go"> left_deletions = 0:</span>
<span class="go"> open_left_deletions = 0,</span>
<span class="go"> extend_left_deletions = 0;</span>
<span class="go"> internal_gaps = 0:</span>
<span class="go"> internal_insertions = 0:</span>
<span class="go"> open_internal_insertions = 0,</span>
<span class="go"> extend_internal_insertions = 0;</span>
<span class="go"> internal_deletions = 0:</span>
<span class="go"> open_internal_deletions = 0,</span>
<span class="go"> extend_internal_deletions = 0;</span>
<span class="go"> right_gaps = 0:</span>
<span class="go"> right_insertions = 0:</span>
<span class="go"> open_right_insertions = 0,</span>
<span class="go"> extend_right_insertions = 0;</span>
<span class="go"> right_deletions = 0:</span>
<span class="go"> open_right_deletions = 0,</span>
<span class="go"> extend_right_deletions = 0.</span>
</pre></div>
</div>
<p>Note that the pairwise aligner in the argument to <code class="docutils literal notranslate"><span class="pre">counts</span></code> does not need to
be the same as aligner that was used the create the alignment.</p>
<p>For an alignment of more than two sequences, the number of identities,
mismatches, and gaps are calculated and summed for all pairs of sequences in
the alignment.</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
<span class="go"> 1 CGGTTTTT 9</span>
<span class="go"> 0 AG-TTT-- 5</span>
<span class="go"> 0 AGGTTT-- 6</span>
<span class="gp">>>> </span><span class="n">counts</span> <span class="o">=</span> <span class="n">alignment</span><span class="o">.</span><span class="n">counts</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">aligned</span>
<span class="go">16</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">identities</span>
<span class="go">14</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">mismatches</span>
<span class="go">2</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">insertions</span>
<span class="go">1</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">deletions</span>
<span class="go">5</span>
</pre></div>
</div>
<p>Here, insertions are defined as sequence insertions of a later sequence into an
earlier sequence in the alignment. In contrast to the pairwise alignment above,
the distinction between insertions and deletions may not be meaningful for a
multiple sequence alignment, and you will probably be more interested in the
number of gaps (= insertions + deletions):</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">gaps</span>
<span class="go">6</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">left_gaps</span>
<span class="go">0</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">right_gaps</span>
<span class="go">4</span>
<span class="gp">>>> </span><span class="n">counts</span><span class="o">.</span><span class="n">internal_gaps</span>
<span class="go">2</span>
</pre></div>
</div>
<p>An <code class="docutils literal notranslate"><span class="pre">AlignmentCounts</span></code> object has the following properties:</p>
<table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p><strong>property</strong></p></th>
<th class="head"><p><strong>description</strong></p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">score</span></code></p></td>
<td><p>Alignment score, or <code class="docutils literal notranslate"><span class="pre">None</span></code> if unknown</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">substitution_score</span></code></p></td>
<td><p>Total substitution score of letters aligned to each other, or <code class="docutils literal notranslate"><span class="pre">None</span></code> if unknown</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">gap_score</span></code></p></td>
<td><p>Total gap score, or <code class="docutils literal notranslate"><span class="pre">None</span></code> if unknown</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">aligned</span></code></p></td>
<td><p>The number of aligned letters in the alignment. This quantity is also calculated if some or all of the sequences are undefined. If all sequences are known, then <code class="docutils literal notranslate"><span class="pre">aligned</span></code> = <code class="docutils literal notranslate"><span class="pre">identities</span></code> + <code class="docutils literal notranslate"><span class="pre">mismatches</span></code>. If some sequences are undefined, then <code class="docutils literal notranslate"><span class="pre">aligned</span></code> > <code class="docutils literal notranslate"><span class="pre">identities</span></code> + <code class="docutils literal notranslate"><span class="pre">mismatches</span></code>.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">identities</span></code></p></td>
<td><p>Number of matched letters in the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">mismatches</span></code></p></td>
<td><p>Number of mismatched letters in the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">positives</span></code></p></td>
<td><p>Number of aligned letters with a positive substitution score</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">gaps</span></code></p></td>
<td><p>Total gap length</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">open_gaps</span></code></p></td>
<td><p>Number of gaps opened in the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">extend_gaps</span></code></p></td>
<td><p>Number of gap extensions in the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">insertions</span></code></p></td>
<td><p>Total number of letters inserted</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">open_insertions</span></code></p></td>
<td><p>Number of insertion gaps opened in the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">extend_insertions</span></code></p></td>
<td><p>Number of insertion gap extensions in the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">deletions</span></code></p></td>
<td><p>Total number of letters deleted</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">open_deletions</span></code></p></td>
<td><p>Number of deletion gaps opened in the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">extend_deletions</span></code></p></td>
<td><p>Number of deletion gap extensions in the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">left_gaps</span></code></p></td>
<td><p>Total gap length on the left side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">open_left_gaps</span></code></p></td>
<td><p>Number of gaps opened on the left side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">extend_left_gaps</span></code></p></td>
<td><p>Number of gap extensions on the left side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">left_insertions</span></code></p></td>
<td><p>Number of letters inserted on the left side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">open_left_insertions</span></code></p></td>
<td><p>Number of insertion gaps opened on the left side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">extend_left_insertions</span></code></p></td>
<td><p>Number of insertion gap extensions on the left side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">left_deletions</span></code></p></td>
<td><p>Number of characters deleted on the left side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">open_left_deletions</span></code></p></td>
<td><p>The number of deletion gaps opened on the left side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">extend_left_deletions</span></code></p></td>
<td><p>Number of deletion gap extensions on the left side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">internal_gaps</span></code></p></td>
<td><p>Total length of gaps within the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">open_internal_gaps</span></code></p></td>
<td><p>Number of gaps opened in the interior of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">extend_internal_gaps</span></code></p></td>
<td><p>Number of gap extensions in the interior of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">internal_insertions</span></code></p></td>
<td><p>Number of letters inserted in the interior of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">open_internal_insertions</span></code></p></td>
<td><p>Number of insertion gaps opened in the interior of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">extend_internal_insertions</span></code></p></td>
<td><p>Number of insertion gas extensions in the interior of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">internal_deletions</span></code></p></td>
<td><p>Number of characters deleted from the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">open_internal_deletions</span></code></p></td>
<td><p>Number of deletion gaps opened in the interior of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">extend_internal_deletions</span></code></p></td>
<td><p>Number of deletion gap extensions in the interior of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">right_gaps</span></code></p></td>
<td><p>Total gap length on the right side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">open_right_gaps</span></code></p></td>
<td><p>Number of gaps opened on the right side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">extend_right_gaps</span></code></p></td>
<td><p>Number of gap extensions on the right side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">right_insertions</span></code></p></td>
<td><p>Number of letters inserted on the right side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">open_right_insertions</span></code></p></td>
<td><p>The number of insertion gaps opened on the right side of the alignment</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">extend_right_insertions</span></code></p></td>
<td><p>The number of insertion gap extensions on the right side of the alignment</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">right_deletions</span></code></p></td>
<td><p>Number of letters deleted on the right side of the alignment</p></td>
</tr>