Now I have a collection of sequences that are derived from cDNAs, but most of them are partial. I can start aligning them, but I'd prefer to use the protein sequences as the guide of alignments (so that indels are multiples of three).
With scripting, perhaps I can predict the peptide from cDNA, align the peptides using CLUSTALW, and convert the peptide alignment back to the DNA alignment - but that's a bit of work.
Is there any alignment program that is aware of codons?