Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes.

ABSTRACT: Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets or expanding the analyses to larger scales. Automated orthology inference should allow such large-scale analyses, but substantial differences between orthologous groups generated by different approaches are observed. We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regard to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes)

SUBMITTER: Deutekom ES 

PROVIDER: S-EPMC8138875 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature