PyFAMSA |Stars| =============== .. |Stars| image:: https://img.shields.io/github/stars/althonos/pyfamsa.svg?style=social&maxAge=3600&label=Star :target: https://github.com/althonos/pyfamsa/stargazers `Cython `_ *bindings and Python interface to* `FAMSA `_, *an algorithm for ultra-scale multiple sequence alignments.* |Actions| |Coverage| |PyPI| |Bioconda| |AUR| |Wheel| |Versions| |Implementations| |License| |Source| |Mirror| |Issues| |Docs| |Changelog| |Downloads| .. |Actions| image:: https://img.shields.io/github/actions/workflow/status/althonos/pyfamsa/test.yml?branch=main&logo=github&style=flat-square&maxAge=300 :target: https://github.com/althonos/pyfamsa/actions .. |Coverage| image:: https://img.shields.io/codecov/c/gh/althonos/pyfamsa/branch/main.svg?style=flat-square&maxAge=600 :target: https://codecov.io/gh/althonos/pyfamsa/ .. |PyPI| image:: https://img.shields.io/pypi/v/pyfamsa.svg?style=flat-square&maxAge=3600 :target: https://pypi.python.org/pypi/pyfamsa .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/pyfamsa?style=flat-square&maxAge=3600 :target: https://anaconda.org/bioconda/pyfamsa .. |AUR| image:: https://img.shields.io/aur/version/python-pyfamsa?logo=archlinux&style=flat-square&maxAge=3600 :target: https://aur.archlinux.org/packages/python-pyfamsa .. |Wheel| image:: https://img.shields.io/pypi/wheel/pyfamsa?style=flat-square&maxAge=3600 :target: https://pypi.org/project/pyfamsa/#files .. |Versions| image:: https://img.shields.io/pypi/pyversions/pyfamsa.svg?style=flat-square&maxAge=3600 :target: https://pypi.org/project/pyfamsa/#files .. |Implementations| image:: https://img.shields.io/pypi/implementation/pyfamsa.svg?style=flat-square&maxAge=3600&label=impl :target: https://pypi.org/project/pyfamsa/#files .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=2678400 :target: https://choosealicense.com/licenses/gpl-3.0/ .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square :target: https://github.com/althonos/pyfamsa/ .. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400 :target: https://git.embl.de/larralde/pyfamsa/ .. |Issues| image:: https://img.shields.io/github/issues/althonos/pyfamsa.svg?style=flat-square&maxAge=600 :target: https://github.com/althonos/pyfamsa/issues .. |Docs| image:: https://img.shields.io/readthedocs/pyfamsa?style=flat-square&maxAge=3600 :target: http://pyfamsa.readthedocs.io/en/stable/?badge=stable .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square :target: https://github.com/althonos/pyfamsa/blob/main/CHANGELOG.md .. |Downloads| image:: https://img.shields.io/pypi/dm/pyfamsa?style=flat-square&color=303f9f&maxAge=86400&label=downloads :target: https://pepy.tech/project/pyfamsa Overview -------- `FAMSA `_ is a method published in 2016 by Deorowicz *et al.* for large-scale multiple sequence alignments. It uses state-of-the-art time and memory optimizations as well as a fast guide tree heuristic to reach very high performance and accuracy. ``pyfamsa`` is a Python module that provides bindings to FAMSA using the `Cython `_ language. It implements a user-friendly, Pythonic interface to align protein sequences using different parameters and access results directly. It interacts with the FAMSA library interface, which has the following advantages: .. grid:: 1 2 3 3 :gutter: 1 .. grid-item-card:: :fas:`battery-full` Batteries-included Just add ``pyfamsa`` as a ``pip`` or ``conda`` dependency, no need for the FAMSA binary or any external dependency. .. grid-item-card:: :fas:`screwdriver-wrench` Flexible Create input `~pyfamsa.Sequence` objects programmatically through the :doc:`Python API `. .. grid-item-card:: :fas:`gears` Practical Retrieve alignments as dedicated `~pyfamsa.Alignment` objects using the compressed gap representation from FAMSA. .. grid-item-card:: :fas:`server` Parallel Run computations in parallel using the FAMSA threading model built on POSIX threads. .. grid-item-card:: :fas:`check` Consistent Get the same results as the latest FAMSA version (``2.2.0``). .. grid-item-card:: :fas:`toolbox` Feature-complete Access all the features of the original CLI through the :doc:`Python API `. Setup ----- Run ``pip install pyfamsa`` 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 ``pyfamsa``. Library ------- .. toctree:: :maxdepth: 2 User Guide 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 `GNU General Public License v3.0 `_. FAMSA is developed by the `REFRESH Bioinformatics Group `_ 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 FAMSA authors. It was developed by* `Martin Larralde `_ *during his PhD project at the* `European Molecular Biology Laboratory `_ *in the* `Zeller team `_.