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BioJava 5: A community driven open-source bioinformatics library

DOI: 10.1371/journal.pcbi.1006791 DOI Help

Authors: Aleix Lafita (European Molecular Biology Laboratory, European Bioinformatics Institute) , Spencer Bliven (Zurich University of Applied Sciences (ZHAW)) , Andreas Prlić (University of California, San Diego) , Dmytro Guzenko (University of California, San Diego) , Peter W. Rose (University of California, San Diego) , Anthony Bradley (University of Oxford; Diamond Light Source) , Paolo Pavan (Genomnia srl) , Douglas Myers-Turnbull (University of California, San Francisco) , Yana Valasatava (University of California, San Diego) , Michael Heuer (University of California Berkeley) , Matt Larson (DNASTAR) , Stephen Burley (University of California, San Diego; Rutgers, The State University of New Jersey; Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School) , Jose M. Duarte (University of California, San Diego)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Plos Computational Biology , VOL 15

State: Published (Approved)
Published: February 2019

Open Access Open Access

Abstract: 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 (

Journal Keywords: Multiple alignment calculation; Bioinformatics; Structural genomics; Genomic libraries; Protein structure; Sequence alignment; Protein structure comparison; Macromolecules

Subject Areas: Information and Communication Technology, Biology and Bio-materials

Technical Areas:

Added On: 12/02/2019 11:16


Discipline Tags:

Computing & software technologies Information & Communication Technologies Data processing Life Sciences & Biotech

Technical Tags: