Description

.. image:: https://img.shields.io/pypi/v/biopython.svg?logo=pypi :alt: Biopython on the Python Package Index (PyPI) :target: https://pypi.python.org/pypi/biopython .. image:: https://img.shields.io/conda/vn/conda-forge/biopython.svg?logo=conda-forge :alt: Biopython on the Conda package conda-forge channel :target: https://anaconda.org/conda-forge/biopython .. image:: https://results.pre-commit.ci/badge/github/biopython/biopython/master.svg :target: https://results.pre-commit.ci/latest/github/biopython/biopython/master :alt: pre-commit.ci status .. image:: https://img.shields.io/circleci/build/github/biopython/biopython.svg?logo=circleci :alt: Linux testing with CircleCI :target: https://app.circleci.com/pipelines/github/biopython/biopython .. image:: https://img.shields.io/appveyor/ci/biopython/biopython/master.svg?logo=appveyor :alt: Windows testing with AppVeyor :target: https://ci.appveyor.com/project/biopython/biopython/history .. image:: https://img.shields.io/github/actions/workflow/status/biopython/biopython/ci.yml?logo=github-actions :alt: GitHub workflow status :target: https://github.com/biopython/biopython/actions .. image:: https://img.shields.io/codecov/c/github/biopython/biopython/master.svg?logo=codecov :alt: Test coverage on CodeCov :target: https://codecov.io/github/biopython/biopython/ .. image:: https://depsy.org/api/package/pypi/biopython/badge.svg :alt: Research software impact on Depsy :target: https://depsy.org/package/python/biopython .. image:: https://github.com/biopython/biopython/raw/master/Doc/images/biopython_logo_m.png :alt: The Biopython Project :target: https://biopython.org Biopython README file ===================== The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. This README file is intended primarily for people interested in working with the Biopython source code, either one of the releases from the https://biopython.org website, or from our repository on GitHub https://github.com/biopython/biopython Our user-centric documentation, `The Biopython Tutorial and Cookbook, and API documentation <https://biopython.org/docs/latest/>`_, is generated from our repository using Sphinx. The `NEWS <https://github.com/biopython/biopython/blob/master/NEWS.rst>`_ file summarises the changes in each release of Biopython, alongside the `DEPRECATED <https://github.com/biopython/biopython/blob/master/DEPRECATED.rst>`_ file which notes API breakages. The Biopython package is open source software made available under generous terms. Please see the `LICENSE <https://github.com/biopython/biopython/blob/master/LICENSE.rst>`_ file for further details. If you use Biopython in work contributing to a scientific publication, we ask that you cite our application note (below) or one of the module specific publications (listed on our website): Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878 For the impatient ================= Python includes the package management system "pip" which should allow you to install Biopython (and its dependency NumPy if needed), upgrade or uninstall with just one terminal command:: pip install biopython pip install --upgrade biopython pip uninstall biopython Since Biopython 1.70 we have provided pre-compiled binary wheel packages on PyPI for Linux, macOS and Windows. This means pip install should be quick, and not require a compiler. As a developer or potential contributor, you may wish to download, build and install Biopython yourself. This is described below. Python Requirements =================== We currently recommend using Python 3.13 from https://www.python.org Biopython is currently supported and tested on the following Python implementations: - Python 3.10, 3.11, 3.12, 3.13 and 3.14 -- see https://www.python.org - PyPy3.10 v7.3.17 -- or later, see https://www.pypy.org Optional Dependencies ===================== Biopython requires NumPy (see https://www.numpy.org) which will be installed automatically if you install Biopython with pip (see below for compiling Biopython yourself). Depending on which parts of Biopython you plan to use, there are a number of other optional Python dependencies, which can be installed later if needed: - ReportLab, see https://www.reportlab.com/opensource/ (optional) This package is only used in ``Bio.Graphics``, so if you do not need this functionality, you will not need to install this package. - matplotlib, see https://matplotlib.org/ (optional) ``Bio.Phylo`` uses this package to plot phylogenetic trees. - networkx, see https://networkx.github.io/ (optional) and pygraphviz or pydot, see https://pygraphviz.github.io/ and https://code.google.com/p/pydot/ (optional) These packages