HP-Rare performs applies the method to private alleles and hierarchical sampling designs. The software uses rarefaction to compensate for the effect of sample size on estimates of the number of alleles and number of private alleles in samples from hierarchical data.
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Kalinowski ST (2005)
HP-Rare 1.0 : a computer program for performing rarefaction on measures of allelic diversity.
Molecular Ecology Notes 5:187-189.