Many people discuss use of the Ka/Ks value (and likelihood ratio test) to address the protein coding potential of genomic sequence as well as identifying sequences that have undergone positive Darwinian selection. The following paper has one of the better descriptions of how one would accomplish this. One addition I would suggest is the use of "RevTrans" ( Nucleic Acids Res. 2003 Jul 1;31(13):3537-9.) to align the open reading frames.