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Package: polysat
Version: 1.4-1
Date: 2015-08-13
Title: Tools for Polyploid Microsatellite Analysis
Authors@R: person("Lindsay V.", "Clark", email = "lvclark@illinois.edu", role = c("aut", "cre"))
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Imports: methods, stats, utils
Suggests: combinat, ade4, adegenet, ape
Description: 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', 'STRand', and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics are also available. polysat can assist the user in estimating the
ploidy of samples, and it can estimate allele frequencies in
populations, calculate pairwise Fst values based on those frequencies, and
export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also
included for assigning alleles to isoloci in cases where one pair of
microsatellite primers amplifies alleles from two or more independently
segregating isoloci.
License: GPL-2
URL: http://openwetware.org/wiki/Polysat
NeedsCompilation: no
Packaged: 2015-08-18 14:17:24 UTC; lvclark
Repository: CRAN
Date/Publication: 2015-08-18 17:05:57
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providing 
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