Biojava

Biojava is an open-source project that creates a framework for biology-oriented Java-based applications. You will find the project at this home page. The framework is relatively easy to integrate into Java projects, as it has few dependencies to other programs.

The project uses Ant for a build tool, therefore it is somewhat difficult to integrate into a Maven-based workflow.

The two major disadvantages of Biojava are bulk and version problems. The package is relatively large and adds a significant size overhead to small bioinformatics projects. And the various release iterations of Biojava are not entirely compatible, often introducing hard to find bugs and discrepancies in dependent projects. Also, a significant part of the functionality has been moved into the BiojavaX project.

Biojava provides excellent implementations for a number of boilerplate bioinformatics problems such as alignments. Therefore, it is ideally suited for a rapid start on a complex problem. However, for limited or for very specialized problems, it may be worthwhile to provide one’s own implementations of standard bioinformatics problems. This removes yet another dependency, reduces the risk of version conflicts, and makes it easier to control the source code.