PytrimAl |Stars|
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`Cython `_ *bindings and Python interface to* `trimAl `_,
*a tool for automated alignment trimming.*
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Overview
--------
PytrimAl is a Python module that provides bindings to trimAl using
`Cython `_. 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 ` to find other ways to install ``pytrimal``.
Library
-------
.. toctree::
:maxdepth: 2
Installation
Statistics
Examples
Contributing
API Reference
Changelog
License
-------
This library is provided under the `GNU General Public License v3.0 `_.
trimAl is developed by the `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 `_ *during his
PhD project at the* `European Molecular Biology Laboratory `_
*in the* `Zeller team `_.