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United States Department of Agriculture

Agricultural Research Service

Research Project: Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Research

Title: Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

Authors
item Kamvar, Zhian -
item Tabima, Javier -
item Grunwald, Niklaus

Submitted to: PeerJ
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 2, 2014
Publication Date: February 2, 2014
Repository URL: http://dx.doi.org/10.7717/peerj.281
Citation: Kamvar, Z.N., Tabima, J.F., Grunwald, N.J. 2014. Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction. PeerJ. 2:e281.

Interpretive Summary: Analysis of genetic data for popualtions of organisms requires extensive statistical analysis tools. We developed the package 'poppr' for the open source R statistical computing language. 'Poppr' provides several novel tools, particularly with regard to analysis of data from populations that reproduce clonally as is often the case for microbes or protists. Data can be analyzed on a user-defined hierarchy including unlimited levels of subpopulation structure. Several new functions are introduced that allow for convenient graphing. A pdf manual with extensive documentation and manuals is provided.

Technical Abstract: Poppr is an R package for analysis of population genetic data. It extends the adegenet package and provides several novel tools, particularly with regard to analysis of data from admixed, clonal, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx. Data can be analyzed on a user-defined hierarchy including unlimited levels of subpopulation structure. New functions include calculation of Bruvo’s distance, batch analysis of the index of association with several indices of genotypic diversity, clone censoring, and graphing including dendrograms with bootstrap support and minimum spanning networks. A pdf manual with extensive documentation and manuals is provided.

Last Modified: 9/22/2014
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