Hi - I'm having a problem with hyphy crashing when I try and estimate substitution parameters using a local GTR model for each of 4 different partitions, where the overall rate of each gene can vary, and the tree and mean branch lengths are given (and, to make matters worse, there's gamma distributed rate variation between sites). As you can probably tell, the batch file is rather complicated, so it might be a mistake in that causing the problem... though I guess Hyphy shouldn't crash, anyway.

I would submit this to Bugzilla, but can't, because I haven't got the e-mail with my password (I registered about 5 hours ago)..

Maybe I could e-mail you the batch and data files (and the messages.log, though I don't think that helps in this case)?

Thanks,

James

(my e-mail is james.cotton@nhm.ac.uk)