BioJava:Download 3.0.1

This page offers downloads for the BioJava 3.0.1 release.

BioJava 3.0.1 requires Java 1.6 or later.


BioJava 3.0.1 has been released and is available using Maven from

Over the last year BioJava has undergone a major re-write. It has been modularized into small, re-usable components and a number of new features have been added. The new approach, modeled after the apache commons, minimizes dependencies and allows for easier contribution of new components.

The 3.0.1 release is mainly a bug fix release for the recent 3.0 released which provided a major rewrite of the biojava code base.

View the page for a list of current modules.

Maven Download

BioJava 3.0.1 requires Maven for the build process. We are providing a BioJava specific Maven repository at .

You can add the BioJava repository by adding the following XML to your project .pom file:

            <name>BioJava repository</name>

Manual Download

.tar.gz containing all jars, source and javadocs: biojava3.0.1-all

Module Binary Jar Source Jar Javadoc Jar
biojava3-core biojava3-core-3.0.1.jar biojava3-core-3.0.1-sources.jar biojava3-core-3.0.1-javadoc.jar
biojava3-alignment biojava3-alignment-3.0.1.jar biojava3-alignment-3.0.1-sources.jar biojava3-alignment-3.0.1-javadoc.jar
biojava3-genome biojava3-genome-3.0.1.jar biojava3-genome-3.0.1-sources.jar biojava3-genome-3.0.1-javadoc.jar
biojava3-structure biojava3-structure-3.0.1.jar biojava3-structure-3.0.1-sources.jar biojava3-structure-3.0.1-javadoc.jar
biojava3-structure-gui biojava3-structure-gui-3.0.1.jar biojava3-structure-gui-3.0.1-sources.jar biojava3-structure-gui-3.0.1-javadoc.jar
biojava3-phylo biojava3-phylo-3.0.1.jar biojava3-phylo-3.0.1-sources.jar biojava3-phylo-3.0.1-javadoc.jar
biojava3-protmod biojava3-protmod-3.0.1.jar biojava3-protmod-3.0.1-sources.jar biojava3-protmod-3.0.1-javadoc.jar
biojava3-ws biojava3-ws-3.0.1.jar biojava3-ws-3.0.1-sources.jar biojava3-ws-3.0.1-javadoc.jar

Browse API docs

You can also browse the documentation at BioJava 3.0.1 api

Release Date

BioJava 3.0.1 has been released on February 13th, 2011.

Legacy Code

Not every feature of the BioJava 1.X code base was migrated over to BioJava 3.0.1. A modularized version of the 1.X sources is available as a new “biojava-legacy” project in SVN. The current legacy builds are at version 1.8. (also available via Maven)

Getting older versions

  • The legacy release of 3.0 can be found here (requires Java 1.5+)
  • The legacy release of 1.8 can be found here (requires Java 1.5+)
  • The legacy release of 1.7.1 can be found here (requires Java 1.5+)
  • The legacy release of 1.7 can be found here (requires Java 1.5+)
  • The legacy release of 1.6 can be found here (requires Java 1.5+)
  • The legacy release of 1.5 can be found here (requires Java 1.4.2+)
  • The legacy release of 1.4 can be found here
  • The legacy release 1.3 can be found here.
  • Older releases of BioJava can be found in the download area.