Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience.

Original publication

DOI

10.1371/journal.pcbi.1004739

Type

Journal article

Journal

PLoS computational biology

Publication Date

11/02/2016

Volume

12

Addresses

Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom.

Keywords

Computational Biology, Evolution, Molecular, Phylogeny, Selection, Genetic, Molecular Sequence Annotation, Genome, Microbial