Just a short note to point out a shuffle pads bug. It doesn't flush its changes to disk until the next edit is made (of any contig, eg complementing, adding a tag, etc) or until gap4 is closed down. To gap4 the changes are visible immediately, but any external program that reads data from the gap4 database (eg gap2caf) will fail until the changes get flushed to disk properly. It's been fixed in the CVS source tree, but I've no idea when I'll release a new version of Gap4. I'm working on something tentatively called Gap5 at the moment anyway ;-).