PytrimAl |Stars|
================

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`Cython <https://cython.org/>`_ *bindings and Python interface to* `trimAl <http://trimal.cgenomics.org/>`_,
*a tool for automated alignment trimming.*

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Overview
--------

PytrimAl is a Python module that provides bindings to trimAl using
`Cython <https://cython.org/>`_. It directly interacts with the trimAl
internals, which has the following advantages:

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

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

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

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

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

   .. grid-item-card:: :fas:`microchip` Efficient

      Use the full power of your CPU with :wiki:`SIMD` instructions to 
      compute alignment statistics, selected with dynamic dispatch
      on the runtime platform.

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

      Get the same results as the most recent trimAl version 
      (``2.0``, unreleased), tested on a set of gold-standard alignments.

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

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

   .. grid-item-card:: :fas:`circle-exclamation` Fault-tolerant

      Recover errors occuring in trimAl as Python exceptions, including 
      an informative error message.


Setup
-----

Run ``pip install pytrimal`` 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 ``pytrimal``.


Library
-------

.. toctree::
   :maxdepth: 2

   User Guide <guide/index>
   Examples <examples/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/>`_.
trimAl is developed by the `trimAl team <http://trimal.cgenomics.org/trimal_team>`_ 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* `trimAl`_ *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>`_.