Converting To Codons

Question

[Eric]

Hello,

I have a multiple sequence alignment (nucleotide) that I'd like to convert to codons, in order to use the REL package in HyPhy. Any advice on how I can make this conversion?

Thanks.

Answer 1

[David W]

You've probably already done it!

For codon models, HyPhy presmues a DNA alignment is "in frame" (ie first codon starts at first first base of alignment). You can check your alignment is in frame using, say, ORF Finder. If the alignment has stop codons or frame-shifts you can use a codon-aware aligner like Prank.

[Eric]

You're right. Thanks.