I'm a Computer Science undergraduate writing my thesis which is about analyzing open source bioinformatics projects and extracting standalone modules. I need those projects to be written in Java and preferably be stable or mature. So far I've found a bunch of projects via SourceForge and I was wondering if there are any notable ones that are not hosted there. A different repository that has a bioinformatics category would be helpful too.

Here's a list of the most promising projects I have so far:

 - Jenetics
 - JGap
 - Jmol
 - Juicebox
 - Picard
 - RDP Classifier
 - Shim
 - Tassel
 - The Chemistry Development Kit
 - Toxfree
 - TreeView
 - VarScan


Thanks in advance.
[JEnsembl][1] is a JAVA API for Ensembl.

[Contrail][2] and [Cloudbase][3] are assemblers. The latter got some new life when an enterprising programmer [retooled it for GPUs][4].

 [1]: http://jensembl.sourceforge.net/
 [2]: http://contrail-bio.svn.sourceforge.net/
 [3]: https://github.com/ice91/CloudBrush
 [4]: https://github.com/zenlc2000/CloudbrushGPU