pangolin.html

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    <h1>pangolin</h1>
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    <h5 style="text-align: left; vertical-align: middle;">Phylogenetic Assignment of Named Global Outbreak Lineages</h5>
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      <img src="../assets/images/pangolin_logo.svg" style="max-height:200px;max-width:220px" alt="" />
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  <p>Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences.</p>
  <p>It is available as a command line tool and a web application. The web application was developed by the Centre for Genomic Pathogen Surveillance. The command line tool is open source software available under the GNU General Public License v3.0.</p>
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<div class="contrib"><a href="{{ 'resources/pangolin/quick_reference.html' | absolute_url }}">Docs index</a></div>
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  <div class="contrib"><a href="{{ 'resources/pangolin/pipeline.html' | absolute_url }}">How it works</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/installation.html' | absolute_url }}">Installation</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/updating.html' | absolute_url }}">Updating</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/usage.html' | absolute_url }}">Usage</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/output.html' | absolute_url }}">Output</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/pangolearn.html' | absolute_url }}">PangoLEARN Description</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/requirements.html' | absolute_url }}">Dependencies</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/references.html' | absolute_url }}">References</a></div>
  <div class="contrib"><a href="{{ 'resources/pangolin/tutorial.html' | absolute_url }}">Web App Tutorial</a></div>
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        <a href="https://github.com/cov-lineages/pangolin" class="image"><img src="../assets/images/pangolin_logo.svg" style="max-height:300px;max-width:320px" alt="" /></a>
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        <a href="https://pangolin.cog-uk.io/" class="image"><img src="../assets/images/pangolin_app.svg" style="max-height:300px;max-width:320px" alt="" /></a>
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      <h3>Command-line tool</h3>
      <p>GNU General Public License v3.0</p>
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        <h3>Web application</h3>
        <p>Developed by the <a href="https://www.pathogensurveillance.net/">Centre for Genomic Pathogen Surveillance.</a></p>
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