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 biological sequences and 3D structures. The main goal of the project is to facilitate rapid application development for bioinformatics.
We have a Wikipedia page (of course!) in case you would like to know more about the project.
If you use BioJava, 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) 28 (20): 2693-2695.
Other articles include:
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank
Jianjiong Gao, Andreas Prlić, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, Peter W Rose
Bioinformatics (2017) 33 (13): 2047–2049.
BioJava: an open-source framework for bioinformatics
R. C. G. Holland, T. A. Down, M. Pocock, A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer, M. J. Schreiber
Bioinformatics (2008) 24 (18): 2096–2097.
BioJava: open source components for bioinformatics
Matthew Pocock; Thomas Down; Tim Hubbard
ACM SIGBIO Newsletter (2000) 20 (2): 10-12.