July 16, 2025Open Access

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

DEDavid EmmsInstitute on Taxation and Economic Policy YLYi LiuUniversity of Oxford LBLaurence J. BelcherUniversity of Oxford

Key Points

OrthoFinder improves the accuracy of orthogroup inference by 7%, contributing to more reliable comparative genomics.
The method's new gene assignment reduces RAM usage while maintaining accuracy, facilitating larger datasets.
Enhanced phylogenetic delineation of orthogroups is central to OrthoFinder's advanced capability and scalability.
This update makes OrthoFinder a more efficient tool for researchers in genomics and evolutionary biology.

Abstract

Here, we present a major advance 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 at https://github.com/OrthoFinder/OrthoFinder.

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