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<span id="contents"></span><h1>Welcome to PyCogent’s documentation!<a class="headerlink" href="#welcome-to-pycogent-s-documentation" title="Permalink to this headline">¶</a></h1>
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<li class="toctree-l1"><a class="reference internal" href="install.html">Quick installation</a></li>
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<div class="section" id="overview">
<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
<p>PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.</p>
<p>Our primary goal is to provide a collection of rigourously validated tools for the manipulation and analysis of genome biology data sets. The project is routinely employed in numerous labs across the world and has provided essential capabilities for many high profile publications, e.g. <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/19043404?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">Nature 2009 457:480-4</a>, <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/19004758?ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">PNAS 2008 105:17994-9</a>, <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/18497261?ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">Science 2008 320:1647-51</a>, <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/18464734?dopt=Citation">Nature 2008 453: 175-83</a> and <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/17828264?dopt=Citation">Nat Genet 2007 39: 1261-5</a>.</p>
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<div class="section" id="contacts-and-contributing">
<h2>Contacts and contributing<a class="headerlink" href="#contacts-and-contributing" title="Permalink to this headline">¶</a></h2>
<p>If you find a bug, have feature or documentation requests then please post comments on the corresponding <a class="reference external" href="http://sourceforge.net/tracker2/?group_id=186234">tracker</a> page at sourceforge. If you have any questions please post on the appropriate projects <a class="reference external" href="http://sourceforge.net/projects/pycogent/forums">forums</a> page at sourceforge. We appreciate your input!</p>
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<div class="section" id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this headline">¶</a></h2>
<p>If you use this software for published work please cite – <a class="reference external" href="http://genomebiology.com/2007/8/8/R171">Knight et al., 2007, Genome Biol, 8, R171</a>.</p>
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<h2>News and Announcements<a class="headerlink" href="#news-and-announcements" title="Permalink to this headline">¶</a></h2>
<p>PyCogent News and Annoucements are available via the News and Announcements Blog at <a class="reference external" href="http://pycogent.wordpress.com">http://pycogent.wordpress.com</a>.</p>
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<li><a class="reference internal" href="#">Welcome to PyCogent’s documentation!</a><ul>
<li><a class="reference internal" href="#overview">Overview</a></li>
<li><a class="reference internal" href="#contacts-and-contributing">Contacts and contributing</a></li>
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