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.
 - [Biojava][1]
 - [Seqmonk][2]
 - [GSEA][3]
 
 [1]: http://biojava.org/wiki/Main_Page
 [2]: http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
 [3]: http://software.broadinstitute.org/gsea/index.jsp