How can I convert genome-wide protein alignments to codon alignments?

More Gareth Anthony Pearson's questions See All

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Diego Santos-Garcia

I use a wrapper script for this purpose: first use transeq to tranlate your DNA to proteins, second align the proteins with MAFFT and finally use pal2nal to aling in a codno-fashion manner.

Nilanjan Roy

More information about availability of programs license ( free or paid) web site and yes may be script in personal email

Sorry for the delay. All software are free of charge.

MAFFT: http://mafft.cbrc.jp/alignment/software/

PAL2ANAL: http://www.bork.embl.de/pal2nal/#Download

Transeq is from the emboos packages that are in all repositories from different linux dsitributions.

About the script, because I'm using one that in not mine, I can not send it. But when I have some free time maybe I can do it.