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sbliven Fix test failure due to PDB change
4LNC was updated to remove the X-Ray experimental method.
This switches the test to 6F2Q, which uses both Neutron & Xray.
Latest commit fd4f8ef Jun 15, 2018
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biojava-aa-prop Next dev cycle for master May 22, 2018
biojava-alignment Next dev cycle for master May 22, 2018
biojava-core Next dev cycle for master May 22, 2018
biojava-genome Next dev cycle for master May 22, 2018
biojava-integrationtest Next dev cycle for master May 22, 2018
biojava-modfinder Next dev cycle for master May 22, 2018
biojava-ontology #731 OBO Parser: replaced_by (#773) Jun 1, 2018
biojava-protein-comparison-tool upgrading version nr. for some reason this was still on an old version. Mar 18, 2016
biojava-protein-disorder Next dev cycle for master May 22, 2018
biojava-structure-gui Next dev cycle for master May 22, 2018
biojava-structure Fix test failure due to PDB change Jun 15, 2018
biojava-survival Next dev cycle for master May 22, 2018
biojava-ws Next dev cycle for master May 22, 2018
development Add license to all files Mar 14, 2018
.gitattributes Comprehensive extension list in .gitattributes Apr 26, 2017
.gitignore ignore *~ files Jan 4, 2015
.travis.yml Another attempt at fixing travis outdated jvm Jul 8, 2017 Fill in the commit and contributor number Mar 22, 2018 Adding initial contributing guidelines, #699 Mar 1, 2018
HEADER.txt Adding header file and modified addlicense script to read from it Mar 12, 2018
KEYS Adding my key #447 Apr 4, 2016
LICENSE Standard LGPL license as provided by github template Mar 10, 2018 New support file, #700 Mar 1, 2018
icon.png updating icon to new official BioJava logo Jul 18, 2016
ignore.txt moving the last ant based trunk to a branch Sep 15, 2009
logo-full.png Add full name BioJava logo Jan 11, 2017
pom.xml Next dev cycle for master May 22, 2018 Update May 23, 2018
travis-settings.xml now using multiple names for specifying ossrh server - this is due to… Apr 11, 2017

Welcome to

Build Status Version License Join the chat at

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

Please visit our homepage.


The BioJava tutorial is a great place to get started. It is most complete for the biojava-structure module.

The BioJava Cookbook contains an older and slightly outdated collection of simple examples that teach the basics for how to work with BioJava.

Full javadocs are available at the BioJava website.

Maven Repository

BioJava release are available from Maven Central. Snapshot builds are distributed using OSS Sonatype

Quick Installation

If you are using Maven you can add the BioJava repository by adding the following XML to your project pom.xml file:

      <!-- other biojava jars as needed -->

Snapshot builds

To use the latest builds from BioJava, you can add the following config your project's pom.xml:


Mailing Lists

BioJava has one main mailing list. In order to avoid SPAM the list only accepts postings from list members. Anybody can become a list member, so please subscribe before you post. If you send without being subscribed your mail might get stuck in the moderation loop, which can cause several weeks of delay (no fun to read through all that spam).

biojava-l general discussion list

This list is intended for general discussion, advice, questions, offers of help, announcements, expressions of appreciation, bugs found in release code and requests for features.

biojava-dev developers list

A dev mailing list used to exist, but it has now been shut down. For dev discussions we now use github issues. Please search existing issues and if you don't find the answer to your question submit a new issue.

Please cite

BioJava: an open-source framework for bioinformatics in 2012
Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
Bioinformatics (2012) 28 (20): 2693-2695.
doi pubmed