Article
 

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

Public Deposited

Contenu téléchargeable

Télécharger le fichier PDF
https://ir.library.oregonstate.edu/concern/articles/th83m110n

Descriptions

Attribute NameValues
Creator
Abstract
  • 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/.
  • Keywords: Clone correction, Microbiology, Genotypic diversity, Genetics, Bootstrap, Computational Science, Bioinformatics, Population genetics, Hierarchy, Mycology, Clonality, Permutation, Minimum spanning networks, Index of association, Bruvo’s distance
  • 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/.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Kamvar, Z. N., Tabima, J. F., Grünwald, N. J. (2014). Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ, 2, e281. doi:10.7717/peerj.281
Journal Title
Journal Volume
  • 2
Déclaration de droits
Funding Statement (additional comments about funding)
  • The work was funded in part by USDA ARS and USDA NIFA.
Publisher
Peer Reviewed
Language
Replaces

Des relations

Parents:

This work has no parents.

Articles

La vignette Titre Date de téléchargement Visibilité actes
file details KamvarZhianBotanyPlantPathologyPopprRPackage.pdf 2017-07-26 Public Télécharger