Tajima's Test of Neutrality

Selection | Tajima’s Test of Neutrality

This conducts Tajima’s test of neutrality (Tajima 1989Tajima_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)Nei_and_Kumar_2000 (page 260-261) for further description.