Package: polysat
Version: 1.5-0
Date: 2016-07-17
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, grDevices, graphics
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: https://github.com/lvclark/polysat/wiki
NeedsCompilation: no
Packaged: 2016-07-17 23:16:59 UTC; Lindsay
Repository: CRAN
Date/Publication: 2016-07-18 13:27:55
