I am knew to bioinformatics and I would like to know if it is possible to run the snpeff on protein sequence? I have successfully identified the variant by nucleotide position, but i want to know the codon for each of my sequences. My goal is to identify residue mutation at specific positions. For example, i obtained these results:
nucleotide position | reference | alternative | mutation
226 C T,A p.Leu76Phe p.Leu76Ile
227 T G,C p.Leu76Arg p.Leu76Pro
228 T A p.Leu76Leu
The problem is that it gives me all the possible residues but the codon may not be found in my real aligned sequences. Can i extract the codon for each of the sequences to have residue information? Also can i extract the frequency of each codon in all my sequences per position?