StAMPP: Statistical Analysis of Mixed Ploidy Populations

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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.

Author
LW Pembleton
Date of publication
2015-07-06 06:31:23
Maintainer
LW Pembleton <luke.pembleton@ecodev.vic.gov.au>
License
GPL-3
Version
1.4

View on CRAN

Man pages

potato
Example genotype input format
potato.mini
Smaller example genotype input format
stampp2genlight
Convert StAMPP genotype data to genlight object
stamppAmova
Analysis of Molecular Variance
stamppConvert
Import and Convert
stamppFst
Fst Computation
stamppGmatrix
Genomic Relationship Calculation
stamppNeisD
Genetic Distance Calculation
StAMPP-package
Statistical Analysis of Mixed Ploidy Populations
stamppPhylip
Export to Phylip Format

Files in this package

StAMPP
StAMPP/inst
StAMPP/inst/CITATION
StAMPP/NAMESPACE
StAMPP/data
StAMPP/data/potato.rda
StAMPP/data/potato.mini.rda
StAMPP/R
StAMPP/R/stamppNeisD.R
StAMPP/R/stamppGmatrix.R
StAMPP/R/stamppFst.R
StAMPP/R/stampp2genlight.R
StAMPP/R/stamppConvert.R
StAMPP/R/stamppAmova.R
StAMPP/R/stamppPhylip.R
StAMPP/MD5
StAMPP/DESCRIPTION
StAMPP/ChangeLog
StAMPP/man
StAMPP/man/stamppFst.Rd
StAMPP/man/stamppConvert.Rd
StAMPP/man/potato.Rd
StAMPP/man/StAMPP-package.Rd
StAMPP/man/stamppPhylip.Rd
StAMPP/man/stamppGmatrix.Rd
StAMPP/man/potato.mini.Rd
StAMPP/man/stamppNeisD.Rd
StAMPP/man/stampp2genlight.Rd
StAMPP/man/stamppAmova.Rd