Rethinking large-scale phylogenomics with EukPhylo v.1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages.

ABSTRACT: Eukaryotic diversity is largely microbial, with macroscopic lineages (plants, animals, and fungi) nesting among a plethora of diverse protists. Our understanding of the evolutionary relationships among eukaryotes is rapidly advancing through 'omics analyses, but phylogenomic analyses are challenging for microeukaryotes, particularly uncultivable lineages, as single-cell sequencing approaches generate a mixture of sequences from hosts, associated microbiomes, and contaminants. Moreover, many analyses of eukaryotic gene families and phylogenies rely on boutique data sets and methods that are challenging for other research groups to replicate. To address these challenges, we present EukPhylo v.1.0, a modular, user-friendly pipeline that enables effective data curation through phylogeny-inform

SUBMITTER: Katz LA 

PROVIDER: S-EPMC12506077 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature