Selection | Tajima’s Test of Neutrality
This conducts Tajima’s test of neutrality (Tajima 1989), which compares the number of segregating sites per site with the nucleotide diversity. (A site is considered segregating if, in a comparison of m sequences, there are two or more nucleotides at that site; nucleotide diversity is defined as the average number of nucleotide differences per site between two sequences). If all the alleles are selectively neutral, then the product 4Nv (where N is the effective population size and v is the mutation rate per site) can be estimated in two ways, and the difference in the estimate obtained provides an indication of non-neutral evolution. Please see Nei and Kumar (2000) (page 260-261) for further description.