haploconfig is a program that can be used to implement tests of neutrality based on the frequency distribution of haplotypes in a sample of DNA sequences (the “haplotype configuration”) and the number of segregating sites. The neutrality tests can be performed conditional on the standard neutral coalescent model with or without recombination, exponential population growth, or island migration.
Rosenberg lab at Stanford University
- Windows / Linux
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Innan H, Zhang K, Marjoram P, Tavaré S, Rosenberg NA.
Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
Genetics 169: 1763-1777 (2005)