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`epitopefinder`_ 
========================================

`epitopefinder`_ is a `Python`_ package for parsing epitopes from data sources such as the `Immune Epitope Database`_, assigning them to specific sites in proteins, and then analyzing the epitopes and their correlations to various other properties.

The program can be run using scripts with text input files, so there is no need to interface directly with the `Python`_ API unless you want to further develop or extend this package. 

The scripts include:

    * The ``epitopefinder_getepitopes.py`` script which identifies epitopes from data files in the format that can be downloaded from the `Immune Epitope Database`_.

    * A variety of analysis scripts which can be used to analyze the output files generated by ``epitopefinder_getepitopes.py``.

There is a section in this documentation describing examples. The files used for these examples can be found in the ``./examples`` subdirectory of the main directory containing `epitopefinder`_ after downloading the package.

`epitopefinder`_ source code is available `on GitHub`_.

`epitopefinder`_ documentation is available `on GitHub Pages`_.

This package was created by `Jesse Bloom`_.


.. toctree::
   :maxdepth: 2

   installation
   mainscripts
   analysisscripts
   examples
   pythonapi
   acknowledgements

.. include:: weblinks.txt