hp-rare 1.0: a computer program for performing rarefaction on measures of allelic richness

By Steven T. Kalinowski. 2005

2,247 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics

View Paper: https://www.semanticscholar.org/paper/34b48d99c3162c1cfc381d5c230ef547bff657ce

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In Ecology, Evolution, Behavior and Systematics

In Genetics

Citations in the corpus

The phylogeographic architecture of the fucoid seaweed Ascophyllum nodosum: an intertidal ‘marine tree’ and survivor of more than one glacial–interglacial cycle (2010, methodology): “0 (Kalinowski, 2005), the number of individuals sequenced or genotyped was plotted against the mean number of alleles/locus or number of haplotypes.”
Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data (2014, methodology): “The mean number of alleles (Na), number of effective alleles (Ne) and unbiased diversity (uh) were computed using GenAlEx 6.4 (Peakall and Smouse, 2006) whereas allelic richness (Rs) was computed using HP-RARE 1.1 (Kalinowski, 2005), which implements the rarefaction method.”
Founder effect and bottleneck signatures in an introduced, insular population of elk (2010, methodology): “Allelic richness (alleles per locus, A) for a given sample size was estimated by counting alleles and by using rarefaction (Kalinowski 2005) to account for differences in sample sizes between populations.”
Low connectivity and declining genetic variability along a depth gradient in Corallium rubrum populations (2011, methodology): “As the number of alleles found in a sample is dependent on sample size, allelic richness (Ar) and private allelic richness (Apr) were calculated by rarefying to a sample size of nine specimens using HP-RARE (Kalinowski 2005).”
ADZE: a rarefaction approach for counting alleles private to combinations of populations (2008, methodology): “In contrast to the methods of Kalinowski (2004, 2005), our approach instead counts alleles required to be found in each of a set of populations, and required to be absent in all other populations.”
Genetic discontinuity among regional populations of Lophelia pertusa in the North Atlantic Ocean (2011, methodology): “As sample sizes at different localities varied, allelic richness, or the number of alleles per locality, was calculated by rarefaction (Kalinowski 2004) to compensate for unequal sample sizes using the program HP-Rare (Kalinowski 2005).”
Responsible genetic approach to stock restoration, sea ranching and stock enhancement of marine fishes and invertebrates (2017, background): “The number of alleles standardized by sample size (allelic richness) offers an additional, and more sensitive, measure of genetic diversity (Kalinowski 2005: Hoban et al. 2014).”