|Logo| PyHMMER |Stars|
======================
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*Cython bindings and Python interface to* `HMMER3 `_.
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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:
.. grid:: 1 2 3 3
:gutter: 1
.. grid-item-card:: :fas:`battery-full` Batteries-included
Just add ``pyhmmer`` as a ``pip`` or ``conda`` dependency, no need
for the HMMER binaries or any external dependency.
.. grid-item-card:: :fas:`screwdriver-wrench` Flexible
Create input `~pyhmmer.easel.Sequence` and `~pyhmmer.plan7.HMM` objects
with the :doc:`API `, or load them from a file.
.. grid-item-card:: :fas:`gears` Practical
Retrieve nested results as dedicated `~pyhmmer.plan7.TopHits` objects,
write them to a file, or use them for further Python analysis.
.. grid-item-card:: :fas:`gauge-high` Fast
Run `hmmsearch` in parallel using an efficient threading model, which
:doc:`outperforms ` HMMER in some typical usecases.
.. grid-item-card:: :fas:`dolly` Shareable
:doc:`Distribute and load ` `~pyhmmer.plan7.HMM`
objects from inside a Python package to facilitate sharing analyses.
.. grid-item-card:: :fas:`eye` Transparent
Access the internals of a `~pyhmmer.plan7.HMM`, inspect the attributes
and manually edit transitions or emissions scores.
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 ` to find other ways to install ``pyhmmer``.
Citation
--------
PyHMMER is scientific software, with a
`published paper `_
in the `Bioinformatics `_. Check the
:doc:`Publications page ` to see how to cite PyHMMER.
Library
-------
.. toctree::
:maxdepth: 2
User Guide
Examples
API Reference
Related Projects
----------------
The following Python libraries may be of interest for bioinformaticians.
.. grid:: 1 3 5 5
:gutter: 1
.. grid-item-card:: :fas:`diamond` PyHMMER
:link: https://pyhmmer.readthedocs.io
Profile Hidden Markov Models (with HMMER).
.. grid-item-card:: :fas:`fire` Pyrodigal
:link: https://pyrodigal.readthedocs.io
Prokaryotic Gene Finding (with Prodigal).
.. grid-item-card:: :fas:`virus-covid` Pyrodigal-gv
:link: https://github.com/althonos/pyrodigal-gv
Pyrodigal for Giant Viruses.
.. grid-item-card:: :fas:`align-center` PyFAMSA
:link: https://pyfamsa.readthedocs.io
Multiple Sequence Alignment (with FAMSA).
.. grid-item-card:: :fas:`scissors` PytrimAl
:link: https://pytrimal.readthedocs.io
Alignment Trimming (with trimAl).
.. grid-item-card:: :fas:`music` LightMotif
:link: https://lightmotif.readthedocs.io
Platform-accelerated motif scoring.
.. grid-item-card:: :fas:`knife;fa-custom` Diced
:link: https://diced.readthedocs.io
CRISPR Detection (with MinCED).
.. grid-item-card:: :fas:`table-cells` Scoring Matrices
:link: https://scoring-matrices.readthedocs.io
Scoring matrices for Cython.
.. grid-item-card:: :fas:`chain` Pyskani
:link: https://pyskani.readthedocs.io
Average Nucleotide Identity (with skani).
.. grid-item-card:: :fas:`forward-fast` PyFastANI
:link: https://pyfastani.readthedocs.io
Average Nucleotide Identity (with FastANI).
.. grid-item-card:: :fas:`magnifying-glass` PyJess
:link: https://pyjess.readthedocs.io
Geometric Template Matching (with Jess).
.. grid-item-card:: :fas:`repeat` PyTantan
:link: https://pytantan.readthedocs.io
Tandem Repeat Masking (with Tantan).
.. grid-item-card:: :fas:`gem` PyOpal
:link: https://pyopal.readthedocs.io
Query/Database Aligner (with Opal).
.. grid-item-card:: :fas:`sword;fa-custom` PySWRD
:link: https://pyswrd.readthedocs.io
Database Heuristic Filtering (with SWORD).
.. grid-item-card:: :fas:`rocket` Mini3di
:link: https://github.com/althonos/mini3di
Protein structure to 3di in pure Python.
.. grid-item-card:: :fas:`calculator` ``peptides.py``
:link: https://peptides.readthedocs.io
Peptide descriptors for Python.
.. grid-item-card:: :fas:`diagram-project` Pronto
:link: https://pronto.readthedocs.io
Open Biomedical Ontologies for Python.
.. grid-item-card:: :fas:`box` NAFcodec
:link: https://nafcodec.readthedocs.io
Nucleotide Archival Format for Python.
.. grid-item-card:: :fas:`bank` ``gb-io.py``
:link: https://gb-io.readthedocs.io
Fast GenBank parser for Python (with ``gb-io``).
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 ` 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 `_.