CRAN/E | polysat

polysat

Tools for Polyploid Microsatellite Analysis

Installation

About

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.

Citation polysat citation info
github.com/lvclark/polysat/wiki

Key Metrics

Version 1.7-7
Published 2022-08-23 584 days ago
Needs compilation? yes
License GPL-2
CRAN checks polysat results

Downloads

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Maintainer

Maintainer

Lindsay V. Clark

Lindsay.Clark@seattlechildrens.org

Authors

Lindsay V. Clark

aut / cre

Alistair J. Hall

ctb

Handunnethi Nihal de Silva

ctb

Tyler William Smith

ctb

Material

NEWS
Reference manual
Package source

Vignettes

Assigning alleles to isoloci in polysat
polysat version 1.7 Tutorial Manual

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

polysat archive

Imports

methods
stats
utils
grDevices
graphics
Rcpp

Suggests

ade4
adegenet
ape

LinkingTo

Rcpp

Reverse Imports

poppr