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

More Gareth Anthony Pearson's questions See All

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How to interpolate from a time-series database ?

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How to run raise regression in R?

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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

dear Diego Santos-Garcia we also need the same soln could you please elaborate more

Dear Dr. Roy, what do you mean with more elaborate? Do you mean to post the script?

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.