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Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

TitlePoppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
Publication TypeJournal Article
2014
AuthorsKamvar, ZN, Tabima, JF, Grünwald, NJ
JournalPeerJ
Volume2
Paginatione281
Date Published3
ISSN2167-8359
Bootstrap, Bruvo's distance, Clonality, Clone correction, genotypic diversity, Hierarchy, Index of association, Minimum spanning networks, Permutation, population genetics

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, 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 formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo's distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under resources at: http://grunwaldlab.cgrb.oregonstate.edu/.

http://dx.doi.org/10.7717/peerj.281
10.7717/peerj.281
Citation Key10.7717/peerj.281
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