Phylogeny on somatic hyper mutations


#41

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?


#42

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.