.. _contents:

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Overview
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``cogent3`` is a software library for genomic biology. It is a fully integrated and thoroughly tested 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>`_ and `non-stationary codon <https://www.ncbi.nlm.nih.gov/pubmed/28175284>`_ models.

**Contents**

.. toctree::
    :maxdepth: 1
    
    warning
    install
    app/index
    draw/index
    library
    licenses

.. note:: All the code presented in this documentation is working, but does not reflect the current best-practice. The documentation will be significantly revised in the next couple of months.

Posting Bugs
============

If you discover a bug please post a ticket at the issues_ page!

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Citation
********

If you use this software for published work please cite -- `Knight et al., 2007, Genome Biol, 8, R171 <http://genomebiology.com/2007/8/8/R171>`_.

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Search
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* :ref:`search`

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Support
*******

We acknowledge the provision by `Wingware <http://wingware.com>`_ of free licenses for their professional IDE. Their commitment, over more than a decade, to supporting our development of Open Source software for science is greatly appreciated. (The port of PyCogent to Python 3 was made much easier by using Wing's refactor tools!)

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