BioJava
The BioJava Project is an open source project dedicated to providing Java tools for processing biological data. This will include objects for manipulating sequences, file parsers, CORBA interoperability, DAS, access to ACeDB, dynamic programming, and simple statistical routines to name just a few things.
The BioJava library is useful for automating those daily and mundane bioinformatics tasks. As the library matures, the BioJava libraries will provide a foundation upon which both free software and commercial packages can be developed.