Skip to content

Home

Jump to bottom Edit New page
Lindsay Clark edited this page Jun 27, 2018 · 9 revisions

polysat is an R package for polyploid microsatellite analysis in ecological genetics. Version 1.7-3 is on CRAN as of June 2018. The development version is here on GitHub.

Version 1.4 introduced some major new functionality for allopolyploids and other organisms in which one microsatellite marker produces alleles from two or more independently segregating isoloci. If you think you have found a bug, please feel free to let me know about it! If I fix the bug but am not immediately ready to release a new version of polysat, I will send you the corrected source code so that you can proceed with your analysis in the meantime.

If you are getting errors or having other problems with polysat, you can contact me and I will try to help you out. Please send your R script and dataset so that I can reproduce the error. I can be contacted at lvclark AT illinois DOT edu.

Tutorials for polysat are available in the inst/doc directory of the package (which is the doc directory of your polysat installation, if you have polysat on your computer). All functions are also documented in the reference manual.

Source code for polysat is available here on GitHub for versions 1.4-1 and later.

What polysat does

  • Assumes allele copy number ambiguity in partial heterozygotes.
  • Handles data of any ploidy, including mixed ploidy samples.
  • Stores genotype data in a simple format that can be easily manipulated to exclude or add samples and loci.
  • Imports and exports data in ABI GeneMapper Genotypes Table, GenoDive, Structure, SPAGeDi, ATetra, Tetrasat/Tetra, POPDIST, and binary presence/absence formats. Import is also available for STRand format, and export is available for adegenet presence/absence format.
  • Calculates pairwise distances between individuals using a stepwise mutation model or infinite alleles model.
  • Calculates Shannon and Simpson indexes of genotype diversity, and can calculate a confidence interval for the Simpson index. Counts alleles for measures of allelic diversity.
  • Counts alleles to assist user in estimating ploidy.
  • Estimates allele frequencies in autopolyploids using either an iterative or non-iterative algorithm. Calculates pairwise FST based on these estimates. Mixed ploidy population size is measured in genomes rather than individuals.
  • Exports allele frequencies in SPAGeDi and adegenet formats.
  • Splits markers into multiple isoloci based on the distribution of genotypes in the population.
  • Easily extensible; ordinary users can write new functions to interface with the package.
Add a custom footer
Add a custom sidebar
Clone this wiki locally