Removing stop codons in alignment using hyphy
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14 months ago
el97004 ▴ 80

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.

hyphy alignment • 579 views
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Entering edit mode
10 weeks ago
Josephy • 0

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.

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