Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

ABSTRACT: Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We fo

SUBMITTER: Lees JA 

PROVIDER: S-EPMC5930550 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature