The EMBOSS support in bioperl-run seems to be version specific. The Freebsd ports tree uses 2.10.0, which doesn't seem to sync. up with the test code very well. I see that there's a 3.0.0 that was released July 15, 2005 on emboss.sourceforge.net/emboss.open-bio.org. Would that be more appropriate? thanks, g.