polysat: Tools for Polyploid Microsatellite Analysis

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 and Polymorphic Information Content are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise or global differentiation statistics 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. polysat is described by Clark and Jasieniuk (2011) <doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2017) <doi:10.1111/1755-0998.12639>.

Version: 1.7-7
Imports: methods, stats, utils, grDevices, graphics, Rcpp
LinkingTo: Rcpp
Suggests: ade4, adegenet, ape
Published: 2022-08-23
DOI: 10.32614/CRAN.package.polysat
Author: Lindsay V. Clark ORCID iD [aut, cre], Alistair J. Hall ORCID iD [ctb], Handunnethi Nihal de Silva [ctb], Tyler William Smith ORCID iD [ctb]
Maintainer: Lindsay V. Clark <Lindsay.Clark at seattlechildrens.org>
License: GPL-2
URL: https://github.com/lvclark/polysat/wiki
NeedsCompilation: yes
Citation: polysat citation info
Materials: NEWS
CRAN checks: polysat results

Documentation:

Reference manual: polysat.html , polysat.pdf
Vignettes: Assigning alleles to isoloci in polysat (source, R code)
polysat version 1.7 Tutorial Manual (source, R code)

Downloads:

Package source: polysat_1.7-7.tar.gz
Windows binaries: r-devel: polysat_1.7-7.zip, r-release: polysat_1.7-7.zip, r-oldrel: polysat_1.7-7.zip
macOS binaries: r-release (arm64): polysat_1.7-7.tgz, r-oldrel (arm64): polysat_1.7-7.tgz, r-release (x86_64): polysat_1.7-7.tgz, r-oldrel (x86_64): polysat_1.7-7.tgz
Old sources: polysat archive

Reverse dependencies:

Reverse imports: poppr

Linking:

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