PyInfernal |Stars|
==================

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*Cython bindings and Python interface to* `Infernal 1.1 <http://eddylab.org/infernal/>`_.

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Overview
--------

`Infernal <https://eddylab.org/infernal>`_ is a biological sequence analysis 
method that uses profile stochastic context-free grammars called 
*covariance models* (CMs) to identify RNA structure and sequence similarities. 
Infernal was developed by `Eric P. Nawrocki <https://scholar.google.com/citations?user=jn84-g0AAAAJ&hl=fr>`_
during his PhD thesis in the `Eddy Laboratory <http://eddylab.org/>`_.

``pyinfernal`` is a Python package, implemented using the `Cython <https://cython.org/>`_
language, that provides bindings to Infernal, directly interacting with the
Infernal internals. It builds on top of `PyHMMER <https://pyhmmer.readthedocs.io>`_, 
and follows a generally similar interface.

Setup
-----

Run ``pip install pyinfernal`` in a shell to download the latest release and all
its dependencies from PyPi, or have a look at the
:doc:`Installation page <guide/install>` to find other ways to install ``pyinfernal``.


Library
-------

.. toctree::
   :maxdepth: 2

   User Guide <guide/index>
   API Reference <api/index>


Related Projects
----------------

The following Python libraries may be of interest for bioinformaticians.

.. include:: related.rst


License
-------

This library is provided under the `MIT License <https://choosealicense.com/licenses/mit/>`_.
The Infernal code is available under
the `BSD 3-clause <https://choosealicense.com/licenses/bsd-3-clause/>`_ license 
which allows redistribution of the sources in the ``pyinfernal`` 
distribution. See the :doc:`Copyright Notice <guide/copyright>` section 
for more information.

*This project is in no way not affiliated, sponsored, or otherwise endorsed by
the original* `Infernal <http://eddylab.org/infernal>`_ *authors. It was developed by*
`Martin Larralde <https://github.com/althonos>`_ *during his PhD project
at the* `Leiden University Medical Center <https://www.lumc.nl/en/>`_
*in the* `Zeller team <https://zellerlab.org>`_.