Codon alignment

[atape]

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

[maubp]

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