pal2nal - 14.1-3 main

PAL2NAL is a program that converts a multiple sequence alignment
of proteins and the corresponding DNA (or mRNA) sequences into
a codon-based DNA alignment. The program automatically assigns
the corresponding codon sequence even if the input DNA sequence
has mismatches with the input protein sequence, or contains UTRs,
polyA tails. It can also deal with frame shifts in the input
alignment, which is suitable for the analysis of pseudogenes.
The resulting codon-based DNA alignment can further be subjected
to the calculation of synonymous (Ks) and non-synonymous (Ka)
substitution rates.