SENDBS computes average nucleotide substitutions within and between populations with standard errors of average nucleotide substitutions estimated with a bootstrap method by resampling sites. Also constructs a population tree with a neighbor-joining method.
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Mol Biol Evol. 1989 May;6(3):290-300.
Variances of the average numbers of nucleotide substitutions within and between populations.
Nei M, Jin L.