BioJava is a mature Open Source project that provides a framework for processing of biological data. BioJava provides tools for parsing common file formats, manipulating sequences and 3D structures. Powerful analysis and statistical routines enable the rapid bioinformatics application development in the Java programming language [http://java.sun.com [http://java.sun.com]]. Here we present the latest BioJava release (version 1.6, released on 13 Apr 2008) which provides improvements in the packages for phylogenetic trees, processing PDB files, and genetic algorithms.

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¹ European Bioinformatics Institute (EMBL-EBI), Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK ² Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge CB2 1QN, UK ³ University Newcaste Upon Tyne, Newcastle Upon Tyne, NE1 7RU, UK ⁴ Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK ⁵ Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK ⁶ Laboratory in Genetics and Genomic Medicine of Inflammation, Montreal, Canada. ⁷ Eberhard Karls University Tübingen, Center for Bioinformatics (ZBIT), Germany ⁸ Harbinger Partners, Inc., St. Paul, Minnesota, USA ⁹ Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos #05-01, Singapore 138670