PytrimAl Stars

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 Installation page to find other ways to install pytrimal.

Library

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.