Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution.

ABSTRACT: Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95 % average nucleotide identity). We r

SUBMITTER: van der Putten BCL 

PROVIDER: S-EPMC9176278 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature