PyFAMSA |Stars|
===============

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`Cython <https://cython.org/>`_ *bindings and Python interface to* `FAMSA <https://github.com/refresh-bio/FAMSA>`_,
*an algorithm for ultra-scale multiple sequence alignments.*

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Overview
--------

`FAMSA <https://github.com/refresh-bio/FAMSA>`_ is a method published in
2016 by Deorowicz *et al.* for large-scale multiple sequence alignments.
It uses state-of-the-art time and memory optimizations as well as a fast
guide tree heuristic to reach very high performance and accuracy.

``pyfamsa`` is a Python module that provides bindings to FAMSA using the
`Cython <https://cython.org/>`_ language. It implements a user-friendly,
Pythonic interface to align protein sequences using different parameters and
access results directly. It interacts with the FAMSA library interface, which
has the following advantages:

.. grid:: 1 2 3 3
   :gutter: 1

   .. grid-item-card:: :fas:`battery-full` Batteries-included

      Just add ``pyfamsa`` as a ``pip`` or ``conda`` dependency, no need
      for the FAMSA binary or any external dependency.

   .. grid-item-card:: :fas:`screwdriver-wrench` Flexible

      Create input `~pyfamsa.Sequence` objects programmatically through 
      the :doc:`Python API <api/index>`.

   .. grid-item-card:: :fas:`gears` Practical

      Retrieve alignments as dedicated `~pyfamsa.Alignment` objects
      using the compressed gap representation from FAMSA.

   .. grid-item-card:: :fas:`server` Parallel

      Run computations in parallel using the FAMSA threading model
      built on POSIX threads.

   .. grid-item-card:: :fas:`check` Consistent

      Get the same results as the latest FAMSA version (``2.2.0``).

   .. grid-item-card:: :fas:`toolbox` Feature-complete

      Access all the features of the original CLI through the :doc:`Python API <api/index>`.



Setup
-----

Run ``pip install pyfamsa`` 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 ``pyfamsa``.


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 `GNU General Public License v3.0 <https://choosealicense.com/licenses/gpl-3.0/>`_.

FAMSA is developed by the `REFRESH Bioinformatics Group <https://refresh-bio.github.io/>`_
and is distributed under the terms of the GPLv3 as well.

*This project is in no way not affiliated, sponsored, or otherwise endorsed by
the original FAMSA authors. It was developed by* `Martin Larralde <https://github.com/althonos>`_ *during his
PhD project at the* `European Molecular Biology Laboratory <https://www.embl.de/>`_
*in the* `Zeller team <https://github.com/zellerlab>`_.