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

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/.Many microbial, fungal, or oomcyete populations violate assumptions for population\ud genetic analysis because these populations are clonal, admixed, partially\ud clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for\ud analyzing data from clonal populations, making analysis difficult and haphazard.\ud We developed the R package poppr providing unique tools for analysis of data from\ud admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for\ud dominant/codominant and haploid/diploid genetic data. Data can be imported from\ud several formats including GenAlEx formatted text files and can be analyzed on a user-defined\ud hierarchy that includes unlimited levels of subpopulation structure and clone\ud censoring. New functions include calculation of Bruvo’s distance for microsatellites,\ud batch-analysis of the index of association with several indices of genotypic diversity,\ud and graphing including dendrograms with bootstrap support and minimum\ud spanning networks. While functions for genotypic diversity and clone censoring are\ud specific for clonal populations, several functions found in poppr are also valuable\ud to analysis of any populations. A manual with documentation and examples is provided.\ud 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/