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Codon alignment

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  • Codon alignment

    I need to make an alignment based of codons, for determining dN/dS ratio in PAML.

    What is a good and reliable way of making it, by using both nucleotide and aa sequences for the alignment?

    For example: Making a protein alignment and determining corresponding codon positions from the nucleotide data.

    Thank you

  • #2
    That's how I would make a codon-aware alignment. I think T-Coffee has an option for this, or you can do it yourself - e.g. I wrote a script to "back translate" or thread the nucleotides onto a protein alignment (with a Galaxy wrapper): https://github.com/peterjc/pico_gala...ign_back_trans

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