Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.

ABSTRACT: To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowin

SUBMITTER: Kamvar ZN 

PROVIDER: S-EPMC4462096 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature