StAMPP: Statistical Analysis of Mixed Ploidy Populations

StAMPP 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. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.

Version: 1.3
Depends: R (≥ 2.14.0), pegas
Imports: parallel, doParallel, foreach, adegenet
Published: 2014-09-01
Author: LW Pembleton
Maintainer: LW Pembleton <luke.pembleton at depi.vic.gov.au>
License: GPL-3
NeedsCompilation: no
Citation: NA
Materials: NA
CRAN checks: StAMPP results

Downloads:

Reference manual: StAMPP.pdf
Package source: StAMPP_1.3.tar.gz
Windows binaries: r-devel: StAMPP_1.3.zip, r-release: StAMPP_1.3.zip, r-oldrel: StAMPP_1.3.zip
OS X Snow Leopard binaries: r-release: StAMPP_1.3.tgz, r-oldrel: StAMPP_1.3.tgz
OS X Mavericks binaries: r-release: StAMPP_1.3.tgz
Old sources: StAMPP archive