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polysat: an R package for polyploid microsatellite analysis


Lindsay V. Clark, Fax: 530 752 4604; E-mail:


We present an R package to help remedy the lack of software for manipulating and analysing autopolyploid and allopolyploid microsatellite data. polysat can handle genotype data of any ploidy, including populations of mixed ploidy, and assumes that allele copy number is always ambiguous in partial heterozygotes. It can import and export genotype data in eight different formats, calculate pairwise distances between individuals using a stepwise mutation and infinite alleles model, estimate ploidy based on allele counts and estimate allele frequencies and pairwise FST values. This software is freely available through the Comprehensive R Archive Network ( and includes a thorough tutorial.