Entering edit mode
9.5 years ago
I am trying to calculate branch specific genetic distances for a bunch of multiple alignments using MEGA command line, but even when I use the user tree phylogenetic tree for my alignments, MEGA produces its own phylogenetic tree topology!
Is there a way I could force MEGA command line to calculate maximum likelihood distances for each branch based on the phylogenetic tree topology which I have specified? Or is there any better command line software for calculating genetic distances for phylogenetic tree branches?
