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The BioJava project

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 and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

BioJava is licensed under LGPL 2.1.

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;

Current Events

Getting BioJava About BioJava Get started with BioJava. Download the latest BioJava release. Get started with BioJava Legacy 1.8. Download BioJava Legacy 1.8.2. Contact us on BioJava Mailing Lists	Documentation BioJava 3.0.5 View simple examples for how to work with BioJava at BioJava:CookBook. Access the documentation for all classes and methods at Javadoc API (v3.0.5) Read some examples of how to use the new BioJava3 code. Coding conventions for BioJava3 Legacy BioJava 1.8.2 Access the documentation for all classes and methods at Javadoc API (v1.8.2) A few tutorials are at BioJava:Tutorial Documentation for the BioJavaX classes: BioJava:BioJavaXDocs Others Dazzle - a Java DAS server library based on BioJava. Java Web Start examples of the BioJava:Performance	CookBook BioJava 3.0.5 BioJava:CookBook - view all cookbook pages Core Protein Structure Pairwise and Multiple Sequence Alignment Genome Sequencing Phylogenetic tree Physico-Chemical Properties Computation Protein Disorder Protein Modification Identification Remote Web Service Calls Legacy BioJava 1.8.2 Legacy CookBook - view all cookbook pages Alphabets and Symbols Basic Sequence Manipulation Translation Proteomics Sequence IO Annotations Locations and Features BLAST and FASTA Counts and Distributions Weight Matrices and Dynamic Programming User interfaces BioSQL and Sequence Databases Genetic Algorithms Ontologies
Community Contact us at the mailing lists. Ask for help, provide feedback here. How to support BioJava. We are looking for Maintainers for some of the modules. Recent changes in this wiki. Who contributed to BioJava? BioJava forum BioJava groups on social networking sites	For Developers Browse through the BioJava repository on Github. Browse BioJava Maven repository. About the BioJava license How to obtain a Git checkout of BioJava. biojava-dev - the mailing list for developers. View open bugs or known issues (old database). Ohloh - The BioJava project metrics at Ohloh.
Applications View a list of applications using BioJava. More than 50 scientific publications reference BioJava. Dazzle - a DAS server library that is based on BioJava.	Thanks The open-bio servers reside in in a Tier 1 Boston area colocation facility. Infrastructure geeks can see pictures of the colocation cage and the new OBF servers online at this URL: [1] -- those servers also host EMBOSS FTP/CVS and mailing lists. We would like to thank Chris Dagdigian from The Bioteam for providing and maintaining the bio* servers. Please see documentation on customizing the interface and the User's Guide for usage and configuration help.