Hello, I have DNA sequences of 51 genes across 7 taxa (I have already aligned the genes with MUSCLE), and I would like to use PAL2NAL to align these sequences to corresponding protein sequences.
My question is:
How to get the protein alignment from my DNA sequences? Should I just translate the whole DNA sequence to protein from the first nucleotide of my sequence (and use the translated protein sequence as my input file in PAL2NAL)? The protein may be different if the codon start from the second and the third nucleotide, so how to know where the codon start?
I really appreciate for any suggestion and help
Pei-Wei