OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability

Nature Methods 2026 Open access

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Authors: David Emms, Yi Liu, Laurence J. Belcher, Jonathan Holmes, Steven Kelly
DOI: 10.1038/s41592-026-03126-6
Cited by: 11
References: 39

Abstract

Here we present a major advancement of the OrthoFinder method. This extends OrthoFinder's high-accuracy comparative genomic framework to provide substantially enhanced scalability and accuracy. Specifically, we show that enhanced phylogenetic delineation of orthogroups provides a 7% relative increase in orthogroup inference accuracy. We further demonstrate that a new gene assignment method substantially reduces overall runtime RAM usage without compromising accuracy. The latest version of OrthoFinder is available via GitHub at https://github.com/OrthoFinder/OrthoFinder .

Fields of Study & Subjects

Genomics and Phylogenetic Studies Genome Rearrangement Algorithms Language and cultural evolution

Publication details

Journal / source
Nature Methods
Publisher
Springer Science and Business Media LLC
Volume
23
Issue
7
Pages
1327–1333
Publication date
9 June 2026
Language
EN