BioJava 5: A community driven open-source bioinformatics library

PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. doi: 10.1371/journal.pcbi.1006791. eCollection 2019 Feb.


BioJava is an open-source project that provides a Java library for processing biological data. The project aims to simplify bioinformatic analyses by implementing parsers, data structures, and algorithms for common tasks in genomics, structural biology, ontologies, phylogenetics, and more. Since 2012, we have released two major versions of the library (4 and 5) that include many new features to tackle challenges with increasingly complex macromolecular structure data. BioJava requires Java 8 or higher and is freely available under the LGPL 2.1 license. The project is hosted on GitHub at More information and documentation can be found online on the BioJava website ( and tutorial ( All inquiries should be directed to the GitHub page or the BioJava mailing list (

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Access to Information
  • Algorithms
  • Computational Biology / methods*
  • Gene Library
  • Genome / genetics
  • Genomics
  • Information Storage and Retrieval
  • Internet
  • Software