StAMPP is an R package for the Statistical Analysis of Mixed Ploidy Populations. It allows users to calculate pairwise Nei’s Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet.
Installation
You can install the latest stable version of StAMPP from CRAN:
install.packages("StAMPP")Version
This GitHub repository hosts the latest version of StAMPP which may be a pre-alpha/alpha/beta development version. Please check NEWS.md for details.
Vignette
A vignette describing the use of the package is available from within R (and also here). Load the package and then use the vignette function.
Citation
LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129.
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