polysat: an R package for polyploid microsatellite analysis

Clark, L.V. and Jasieniuk, M. (2011) polysat: an R package for polyploid microsatellite analysis. Molecular Ecology Resources, 11 (3). pp. 562-566.

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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 (http://cran.r-project.org/) and includes a thorough tutorial.

Item Type: Article
Additional Information: Supporting information: http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.02985.x/suppinfo
Uncontrolled Keywords: allele copy number ambiguity; data conversion; FST; genetic distance; polyploidy; SSR
Author Affiliation: Department of Plant Sciences, Mail Stop 4, University of California, Davis, CA 95616, USA
Subjects: Crop Improvement > Genetics/Genomics
Divisions: General
Depositing User: Mr Siva Shankar
Date Deposited: 19 Mar 2014 03:04
Last Modified: 19 Mar 2014 03:04
Official URL: http://dx.doi.org/10.1111/j.1755-0998.2011.02985.x
URI: http://eprints.icrisat.ac.in/id/eprint/12908

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