Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.
TLDR
The R package poppr is developed providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations, and functions for genotypic diversity and clone censoring are specific for clonal populations.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/.read more
Citations
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Journal ArticleDOI
Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.
TL;DR: Several significant extensions to poppr are provided including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies.
Journal ArticleDOI
vcfr: a package to manipulate and visualize variant call format data in R.
TL;DR: The r package vcfr provides essential, novel tools currently not available in r to facilitate VCF data exploration, including intuitive methods for data quality control and easy export to other r packages for further analysis.
Journal ArticleDOI
stratag: An r package for manipulating, summarizing and analysing population genetic data.
TL;DR: The r package stratag is introduced as a user‐friendly population genetics toolkit that provides easy access to a suite of standard genetic summaries as well as the ability to rapidly manipulate stratified genetic data for custom analyses.
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Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams
TL;DR: The results indicate that the cancer is spreading between animals in the marine environment as a clonal transmissible cell derived from a single original clam, suggesting that horizontal transmission of cancer cells is more widespread in nature than previously supposed.
Journal ArticleDOI
Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing
Alireza Abdolrasouli,Alireza Abdolrasouli,Johanna Rhodes,Mathew A. Beale,Mathew A. Beale,Ferry Hagen,Thomas R. Rogers,Anuradha Chowdhary,Jacques F. Meis,Darius Armstrong-James,Matthew C. Fisher +10 more
TL;DR: In this paper, a whole-genome sequencing (WGS) was performed for high-resolution single-nucleotide polymorphism (SNP) analysis of 24 A. fumigatus isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, the Netherlands, and the United Kingdom, in order to assess the utility of WGS for characterizing the alleles causing resistance.
References
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