.. _contents:


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``cogent3`` Overview
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cogent3_ is a software library for genomic biology. It is a comprehensive framework for manipulation of genomic sequence data and for conducting molecular evolutionary analyses. It is distinguished by many unique built-in capabilities. Of particular note are our non-stationary Markov substitution models. These include `non-stationary nucleotide <https://www.ncbi.nlm.nih.gov/pubmed/25503772>`_,

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and `non-stationary codon <https://www.ncbi.nlm.nih.gov/pubmed/28175284>`_ models. Plus, the ability to manipulate biological sequences by their annotations.

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.. toctree::
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    :maxdepth: 2
    
    warning
    install
    app/index
    draw/index
    library
    licenses
    general

.. _cogent3: https://github.com/cogent3/cogent3
