I've been running several site models on PAML but now I would like to perform the same analyses on HyPhy. I don't know exactly how can I specify to launch the M7 and M8 models from PAML on Hyphy. I tried to use the NielsenYang.bf batch file and I could see that the 16th model under a GY94 substitution model corresponds to the M8a (or M7), but I've not be able to run the M8 model until now. Someone could help?
Thanks in advance!