polysat (1.1-0)
Tools for Polyploid Microsatellite Analysis.
http://openwetware.org/wiki/Polysat
http://cran.r-project.org/web/packages/polysat
polysat is a collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, POPDIST, and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model. It can assist the user in estimating the ploidy of samples, and lastly it can estimate allele frequencies in populations, calculate pairwise Fst values based on those frequencies, and export allele frequencies to SPAGeDi and adegenet.
Maintainer:
Lindsay V. Clark
Author(s): Lindsay V. Clark <lvclark@ucdavis.edu>
License: GPL (>= 2)
Uses: combinat, ade4, adegenet
Released over 2 years ago.
