Removing stop codons in alignment using hyphy

Question

[el97004]

Hi everyone.

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.

Thank you.

Answer 1

[Josephy]

You can use hyphy -i to enter the interactive command line. Then select data tool files in the first step and choose to remove all the stop codons in the input file.