Molecular Ecology Resources

Volume 13, Issue 5 p. 946-952

Resource Article

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

Luke W. Pembleton,

Corresponding Author

Luke W. Pembleton

Department of Environment and Primary Industries, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Dairy Futures Cooperative Research Centre, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

La Trobe University, Bundoora, Vic. 3083, Australia

Correspondence: Luke W. Pembleton, Fax: +61 3 9032 7158; E-mail: [email protected]Search for more papers by this author

Noel O. I. Cogan,

Noel O. I. Cogan

Department of Environment and Primary Industries, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Dairy Futures Cooperative Research Centre, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Search for more papers by this author

John W. Forster,

John W. Forster

Department of Environment and Primary Industries, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Dairy Futures Cooperative Research Centre, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

La Trobe University, Bundoora, Vic. 3083, Australia

Search for more papers by this author

Luke W. Pembleton,

Corresponding Author

Luke W. Pembleton

Department of Environment and Primary Industries, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Dairy Futures Cooperative Research Centre, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

La Trobe University, Bundoora, Vic. 3083, Australia

Correspondence: Luke W. Pembleton, Fax: +61 3 9032 7158; E-mail: [email protected]Search for more papers by this author

Noel O. I. Cogan,

Noel O. I. Cogan

Department of Environment and Primary Industries, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Dairy Futures Cooperative Research Centre, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Search for more papers by this author

John W. Forster,

John W. Forster

Department of Environment and Primary Industries, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

Dairy Futures Cooperative Research Centre, AgriBio, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia

La Trobe University, Bundoora, Vic. 3083, Australia

Search for more papers by this author

First published: 06 June 2013

https://doi.org/10.1111/1755-0998.12129

Citations: 445

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Abstract

Statistical Analysis of Mixed-Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed-ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise F_ST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed-ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high-throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.

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Volume13, Issue5

September 2013

Pages 946-952

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

Abstract

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StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

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Supporting Information

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