I'm trying to remove stop codons from my codon based alignment. Hyphy documentation states that it can do this:
"the HyPhy standard analysis Data File Tools:CleanStopCodons.bf can do this by replacing all stop codons with indels"
I've located the 'CleanStopCodons.bf' here. But I cannot find any information on how I can run it/ usage information. Anyone know how to use this module or how to run .bf files?
I have hyphy installed on command line.