I've written up a quick changelog for the BioJava 1.1 release (which will hopefully be out later today). The emphasis is on major things which have changed since 1.0, and might mean people will have to update code. It's in Wiki, so please add extra items if you think something important is missing (I'm sure there is...) http://www.biojava.org/wiki/html/BioJava/BioJavaChanges.html Happy hacking, Thomas.