Distance | Codon Based Fishers Exact Test
This provides a test of selection based on the comparison of the numbers of synonymous and nonsynonymous substitutions between sequences. Use this command to conduct a small sample test of positive selection (Zhang et al. 1997): a one-tailed Fishers Exact test. If the resulting P -value is less than 0.05, then the null hypothesis of neutral evolution (strictly neutral and purifying selection) is rejected. If the observed number of synonymous differences per synonymous site (pS) exceeds the number of nonsynonymous differences per nonsynonymous site (pN) then MEGA sets P = 1 to indicate purifying selection, rather than positive selection.
See Nei and Kumar (2000) (page 56) for further description and an example.