Phylogeny on somatic hyper mutations


Oh nice! Then I guess you also have the option of ASR under GY94 since your model is compared to that? Are you by any chance using PAML or some variant of that?


Sort of. They can do GY94 while assuming the specified germline sequence is the direct ancestor of the other sequences, as IgPhyML does. And no re: PAML - aside from PDL and some other Perl packages they’re from scratch, just like mom used to make.