I've checked out 1.2 and run the tests. They all pass for me on a fresh checkout. Are you guys sure you don't have a different biojava.jar masking the older classes? If so we may need to fix the build.xml so this can't happen. -- - Keith James <kdj@sanger.ac.uk> bioinformatics programming support - - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -