PyHMMER

Cython bindings and Python interface to HMMER3.

Overview

HMMER is a biological sequence analysis tool that uses profile hidden Markov models to search for sequence homologs. HMMER3 is maintained by members of the the Eddy/Rivas Laboratory at Harvard University.

pyhmmer is a Python module, implemented using the Cython language, that provides bindings to HMMER3. It directly interacts with the HMMER internals, which has the following advantages over CLI wrappers:

Setup

Run pip install pyhmmer 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 pyhmmer.

Citation

PyHMMER is scientific software, with a published paper in the Bioinformatics. Check the :doc:`Publications page <guide/publications>` to see how to cite PyHMMER.

Library

Related Projects

The following Python libraries may be of interest for bioinformaticians.

License

This library is provided under the MIT License. The Easel and HMMER3 codes are available under the BSD and BSD 3-clause licenses respectively, which both allow redistribution of the sources in the pyhmmer distribution. See the :doc:`Copyright Notice <guide/copyright>` section for more information.

This project is in no way not affiliated, sponsored, or otherwise endorsed by the original HMMER authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.