Hello,

I am trying to generate multiple sequence alignments of N- and C-terminal domains (separately) from nucleotide sequences based on a sequence alignment of their encoded proteins. One of my issues is that not all of my nucleotide sequences start in the first codon position and many include either 5' or 3' UTR. Can anyone recommend an automated way to align the nucleotide sequences preserving the amino acid alignment? There are too many sequences to do this manually. Please let me know.

Thank you.