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8.9 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?
