Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference.

ABSTRACT: Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing f

SUBMITTER: Smith ML 

PROVIDER: S-EPMC9178227 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature