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BioJava

Open source

The project is hosted, developed, and maintained on GitHub.

GitHub project

Protein structures

BioJava provides an API to maintain local installations of the PDB, load and manipulate structures, perform standard analysis such as sequence and structure alignments and visualize them in 3D.

Biological sequences

BioJava supports reading and writing popular sequence file formats, translating DNA sequences into proteins and other common bioinformatics routines.

Please cite

BioJava 5: A community driven open-source bioinformatics library
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte
PLOS Computational Biology (2019) 15 (2):e1006791.
doi pubmed

Get in touch

Questions, comments, and communications regarding BioJava can be done either on GitHub or through the BioJava mailing list. Subscribe to stay up to date!

  • Tutorial

    The tutorial offers an introduction into some of the features provided by BioJava.

    Tutorial

  • CookBook

    The Cookbook provides simple coding recipes to common bioinformatics problems using BioJava.

    Cookbook

  • Javadoc API

    The Javadocs for the current BioJava 7.1.4 release.

    Javadoc API

  • Release 7.1.4

    BioJava is available from Maven Central.

    Maven Central

  • Wiki

    All pages from the legacy wiki site have been migrated to markdown pages

    View wiki

  • Legacy Javadoc API

    The Javadocs for BioJava legacy 1.x versions.

    View 1.9.5 API