Polysat

polysat is an R package soon to be released for polyploid microsatellite analysis. Version 0.0 is complete and is being tested before public release.

What polysat does

• Assumes allele copy number ambiguity in partial heterozygotes
• Handles data of any ploidy, including mixed ploidy samples
• Genotype data is stored in a simple format that can be easily manipulated to exclude or add samples and loci
• Import and export of data in ABI GeneMapper Genotypes Table, GenoDive, Structure, ATetra, Tetrasat/Tetra, and binary presence/absence formats.
• Calculates pairwise distances between individuals using a stepwise mutation model or infinite alleles model
• Counts alleles to assist user in estimating ploidy
• Estimates allele frequencies and calculates pairwise F_ST based on these estimates. Mixed ploidy population size is measured in genomes rather than individuals.

Author and Maintainer

User:Lindsay V. Clark

Obtaining polysat

polysat will be submitted to CRAN in the very near future.

Documentation

Tutorial manual:

Reference manual:

How to cite polysat

Clark and Jasieniuk are going to submit a computer program note to Molecular Ecology Resources.

Wish List

This section will list additional functionality requested by users, and my progress towards adding that functionality. Feel free to email me with any requests for what you want polysat to be able to do! If you have created your own functions to interface with the package and would like to be added as a contributor, I am open to that as well.