Annotation of position in an Open Reading Frame from a list of sites

Question

[tim_mci]

Hi all,

I am working human mitochondrial sequence data (predominantly using R). I am looking for a tool to quickly annotate if any given site falls in the 1st, 2nd, or 3rd position in a codon (if they fall in an Open Reading Frame at all). I have full mitochondrial sequences in fasta format, as well as a list of specific sites I am investigating in a csv file.

Thank you in advance!