.. _contents:

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Welcome to PyCogent's documentation!
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**Contents**

.. toctree::
    :maxdepth: 1
    
    install
    README
    coding_guidelines
    examples/index
    developer_notes
    licenses
    ChangeLog

..     cookbook/index # connect back in when release done


.. todolist::

.. todo::

    **FOR RELEASE:** unlink cookbook until it's complete

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Overview
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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.

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. `Nature 2009 457:480-4`_, `PNAS 2008 105:17994-9`_, `Science 2008 320:1647-51`_, `Nature 2008 453: 175-83`_ and `Nat Genet 2007 39: 1261-5`_.

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Contacts and contributing
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If you find a bug, have feature or documentation requests then please post comments on the corresponding tracker_ page at sourceforge. If you have any questions please post on the appropriate projects forums_ page at sourceforge. We appreciate your input!

.. _tracker: http://sourceforge.net/tracker2/?group_id=186234
.. _forums: http://sourceforge.net/forum/?group_id=186234

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Citation
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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`

.. _`Nature 2009 457:480-4`: http://www.ncbi.nlm.nih.gov/pubmed/19043404?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
.. _`PNAS 2008 105:17994-9`: http://www.ncbi.nlm.nih.gov/pubmed/19004758?ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
.. _`Science 2008 320:1647-51`: http://www.ncbi.nlm.nih.gov/pubmed/18497261?ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
.. _`Nature 2008 453: 175-83`: http://www.ncbi.nlm.nih.gov/pubmed/18464734?dopt=Citation
.. _`Nat Genet 2007 39: 1261-5`: http://www.ncbi.nlm.nih.gov/pubmed/17828264?dopt=Citation
