GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.
Java-ML is a collection of machine learning algorithms with a common interface for each type of algorithms. The library is aimed at software engineers and programmers, so no GUI, but clear interfaces. It provides reference implementations for algorithms described in the scientific literature, it has well documented source code and provides plenty of code samples and tutorials.