And the winner is PAML(Phylogenetic Analysis by Maximum Likelihood) by Ziheng Yang!
I thought BioX is the best “bridge” between different programs because it supports so many different format. But PHYLIP and PAUP* format sequences generated by BioX are NOT readable by PAML’s yn00 program, although PAML claim to support PHYLIP and PAUP* nexus.
Well, maybe it is because me who hasn’t found a good way to do this. But you have to write control file for the program to run. And basically every sequence you are going to run, kind of need a different control file. And this is really unbelievable.