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GFam -- Automatic annotation of gene families
=============================================

.. image:: figures/gfam_logo.*
   :height: 63pt
   :width: 202.5pt
   :alt: GFam logo
   :align: center

This is the documentation of ``gfam``, a Python module to aid the automatic
annotation of gene families based on consensus domain architecture, written
by `Tamás Nepusz`_.

GFam has no official publication yet, but there will soon be one. You are
kindly asked to cite the webpage of GFam until an official GFam publication
comes out:

  | **GFam: a platform for automatic annotation of gene families**
  | Tamás Nepusz, Rajkumar Sasidharan, David Swarbreck, Eva Huala and
  | Alberto Paccanaro. <http://github.com/ntamas/gfam>

GFam can generally be considered stable. We have used it successfully to
annotate the whole genome of *Arabidopsis thaliana* and *Arabidopsis lyrata*.
Please email the author_ if you discover any bugs, or feel free to
`submit a bug report`_ on GitHub_.

If you are interested in the latest and greatest (but maybe unstable) version
of GFam, you can get it from GitHub_ - just click on the **Download source**
button on the GitHub_ page.

.. _Tamás Nepusz: http://hal.elte.hu/~nepusz
.. _author: http://www.cs.rhul.ac.uk/home/tamas
.. _GitHub: http://github.com/ntamas/gfam
.. _submit a bug report: http://github.com/ntamas/gfam/issues

.. toctree::
   :maxdepth: 2

   intro
   running
   pipeline
   suppl
   api

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`