# biopython

> Freely available tools for computational molecular biology.

- **URL**: https://www.freshcrate.ai/projects/biopython
- **Author**: pypi
- **Category**: RAG & Memory
- **Latest version**: `master@2026-06-01` (2026-06-01)
- **License**: Unknown
- **Source**: https://github.com/biopython/biopython/
- **Homepage**: https://pypi.org/project/biopython/
- **Language**: Python
- **GitHub**: 4,976 stars, 1,886 forks
- **Registry**: pypi (`biopython`)
- **Tags**: `pypi`

## 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

## Recent releases

| Version | Date | Urgency | Changes |
| --- | --- | --- | --- |
| `master@2026-06-01` | 2026-06-01 | High | Latest activity on master branch |
| `1.87` | 2026-04-21 | Low | Imported from PyPI (1.87) |
| `master@2026-04-14` | 2026-04-14 | Medium | Latest activity on master branch |
| `master@2026-04-14` | 2026-04-14 | Medium | Latest activity on master branch |
| `master@2026-04-14` | 2026-04-14 | Medium | Latest activity on master branch |
| `biopython-187` | 2026-03-30 | Medium | Tag biopython-187 |
| `biopython-186` | 2025-10-28 | Low | Tag biopython-186 |
| `biopython-185` | 2025-01-15 | Low | Tag biopython-185 |
| `biopython-184` | 2024-06-28 | Low | Tag biopython-184 |
| `biopython-183` | 2024-01-10 | Low | Tag biopython-183 |

## Dependency audit

- **Score**: 76/100
- **Total deps**: 1
- **Resolved**: 0
- **Unresolved**: 1
- **License conflicts**: 0
- **Warnings**: 2
- **Scanned**: 2026-05-25

## Citation

- HTML: https://www.freshcrate.ai/projects/biopython
- Markdown: https://www.freshcrate.ai/projects/biopython.md
- Dependencies JSON: https://www.freshcrate.ai/api/projects/biopython/deps

_Generated by freshcrate.ai. Indexes pypi releases for AI-agent ecosystem packages._