biopython

What it is and what it does

Biopython is a mature, production-grade library for computational molecular biology written in Python. It provides modules for reading and writing biological sequence formats, analyzing sequences, accessing biological databases, parsing phylogenetic trees, and generating graphics for molecular data. The package is built on numpy and supports optional dependencies for specialized tasks like phylogenetic visualization and database connectivity.

Developers use Biopython to automate sequence analysis workflows, parse large biological datasets, perform comparative genomics, and integrate bioinformatics into larger Python applications. It is widely adopted in academic research and bioinformatics pipelines, with active community maintenance and support for Python 3.10, 3.11, 3.12, 3.13, 3.14.

Use it for:

• Parse and manipulate biological sequences in standard formats for comparative analysis.
• Query and retrieve biological data from online databases and parse results programmatically.
• Analyze phylogenetic trees and generate visualizations with optional dependencies.
• Build automated bioinformatics pipelines combining sequence analysis and statistical methods.
• Access and query biological data stored in PostgreSQL or MySQL databases via BioSQL module.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Biopython provides Python tools for computational molecular biology, including sequence analysis, structure parsing, database access, and phylogenetic tree manipulation.

Yes, with a license review. Biopython is production-stable, actively maintained, and widely used in computational biology. Install friction is low thanks to pre-compiled wheels for multiple platforms. However, verify that the custom Biopython License Agreement aligns with your project's licensing requirements before committing to it in production or proprietary work.

Install

biopython on PyPI

pip install biopython

uv add biopython

poetry add biopython

Installing biopython

Before you install

Pre-compiled wheels available for Python 3.10, 3.11, 3.12, 3.13 on Linux, macOS, and Windows reduce install friction significantly. Active maintenance with a release 8 days old and 5164 GitHub stars indicate a well-supported project.

License in practice

License treatment is marked unclear; the package uses a custom Biopython License Agreement (LicenseRef-Biopython-License-Agreement) rather than a standard SPDX identifier. Review the LICENSE file on the repository before use in proprietary or restricted contexts.

Quickstart

pip install biopython

import biopython
# Biopython modules available for sequence analysis and database access

Requires numpy, which is installed automatically. Python 3.10 or later required.

Verify before relying

• Exact scope and restrictions of the custom Biopython License Agreement—whether it permits commercial use or has attribution requirements beyond standard open-source terms.
• Whether all optional dependencies (ReportLab, matplotlib, networkx, rdflib, psycopg2, MySQL connectors) are truly optional or required for core functionality.
• Specific sequence formats and biological databases supported by the package.

Package facts

Evidence: biopython-1.88-cp310-cp310-macosx_11_0_arm64.whl; biopython-1.88-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl; biopython-1.88-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl; biopython-1.88-cp310-cp310-win32.whl; biopython-1.88-cp310-cp310-win_amd64.whl; biopython-1.88-cp311-cp311-macosx_11_0_arm64.whl; biopython-1.88-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl; biopython-1.88-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl; biopython-1.88-cp311-cp311-win32.whl; biopython-1.88-cp311-cp311-win_amd64.whl; biopython-1.88-cp312-cp312-macosx_11_0_arm64.whl; biopython-1.88-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl; biopython-1.88-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl; biopython-1.88-cp312-cp312-win32.whl; biopython-1.88-cp312-cp312-win_amd64.whl; biopython-1.88-cp313-cp313-macosx_11_0_arm64.whl; biopython-1.88-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl; biopython-1.88-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl; biopython-1.88-cp313-cp313-win32.whl; biopython-1.88-cp313-cp313-win_amd64.whl

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