Disparity Index measures the observed difference in substitution patterns for a pair of sequences. It works by comparing the nucleotide (or amino acid) frequencies in given pair of sequences and using the number of observed differences between sequences. MEGA 4 computes and presents the Disparity Index per site, which is given by the total disparity index between two sequences divided by the number of positions compared, excluding gaps and missing data. It is more powerful than a chi-square test of the equality of base frequencies between sequences.