tajima89d_test

TAJIMA89D_TEST - Tajima's Test of Neutrality
This function conducts Tajima's test of neutrality (Tajima 1989). Tajima's test 
compares the number of segregating sites per site with the nucleotide diversity.
(A site is considered a segregating site if there are two or more nucleotides 
at that site in a comparison of m sequences, and 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 in 
these two ways provides indication of non-neutral evolution.

Minimum number of sequences in data files: The data file must contain at least 
four sequences. Sites containing alignment gaps (or sites with missing data) 
are not used (these sites are completely excluded).

 Syntax: [d]=tajima89d_test(aln)

 Inputs:
    aln   - Alignment structure

 Outputs:
    d     - Tajima's D statistic


 See also: