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:

- **single dependency**: PytrimAl is distributed as a Python package, so you
  can add it as a dependency to your project, and stop worrying about the
  trimAl binary being present on the end-user machine.
- **no intermediate files**: Everything happens in memory, in a Python object
  you control, so you don't have to invoke the trimAl CLI using a
  sub-process and temporary files. `Alignment` objects can be created
  directly from Python code.
- **friendly interface**: The different trimming methods are implement as
  Python classes that can be configured independently.
- **error management**: Errors occuring in trimAl are converted
  transparently into 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 <install>` to find other ways to install ``pytrimal``.


Library
-------

.. toctree::
   :maxdepth: 2

   Installation <install>
   Statistics <statistics>
   Examples <examples/index>
   Contributing <contributing>
   API Reference <api/index>
   Changelog <changes>


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>`_.