Tools for Polyploid Microsatellite Analysis
Additional Data on Rubus Samples
Assign Alleles to Isoloci Based on Distribution of Genotypes
Retrieve and Count Unique Alleles
Group Individuals Based on a Distance Threshold
Genetic Distance Metric of Bruvo et al.
Distance Measure of Bruvo et al. under Genome Loss and Addition
Estimate Population Differentiation Statistics
Sort Alleles into Isoloci
Remove Samples or Loci from an Object
Estimate Allele Frequencies with EM Algorithm
Edit Genotypes Using the Data Editor
Estimate Ploidies Based on Allele Counts
Find Missing Genotypes
Convert Allele Frequencies for Adegenet
Class "genambig"
Convert Between Genotype Object Classes
Class "genbinary"
Class "gendata"
Convert Data to genind Format
Find All Unique Genotypes for a Locus
Genotype Diversity Statistics
Calculate Probabilities of Unambiguous Genotypes
Determine Whether Genotypes Are Missing
Calculate Band-Sharing Dissimilarity Between Genotypes
Tools for Working With Pairwise Distance Arrays
Mean Pairwise Distance Matrix
Merge Two Genotype Objects into One
Merge Allele Assignment Matrices
Polymorphic Information Content
Accessor, Replacement, and Manipulation Functions for "ploidysuper" ...
Class "ploidysuper" and Subclasses
Perform Allele Assignments across Entire Dataset
Internal Functions in polysat
Read File in ATetra Format
Read GeneMapper Genotypes Tables
Import Genotype Data from GenoDive File
Read Genotype Data in POPDIST Format
Read Genotypes in SPAGeDi Format
Read Genotypes Produced by STRand Software
Read Genotypes and Other Data from a Structure File
Read Data from a TETRASAT Input File
Create a New genambig Dataset with Loci Split into Isoloci
Convert Ploidy Format of a Dataset
Accessor and Replacement Functions for "gendata" Objects
Generate Simulated Datasets
Simple Allele Frequency Estimator
Print Genotypes to the Console
Write Genotypes in ATetra Format
Create a File of Allele Frequencies for SPAGeDi
Write Genotypes to a Table Similarly to ABI GeneMapper
Write a File in GenoDive Format
Write Genotypes to a POPDIST File
Write Genotypes in SPAGeDi Format
Write Genotypes in Structure 2.3 Format
Write Genotype Data in Tetrasat Format
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>.