What question did this study set out to answer?

The central aim is to improve the accuracy and scalability of phylogenetic orthology inference through OrthoFinder.

June 11, 2026Nature Methods0 citationsOpen Access

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability

DEDavid Emms YLYi Liu LBLaurence J. Belcher

Key Points

The central aim is to improve the accuracy and scalability of phylogenetic orthology inference through OrthoFinder.
Enhancement of phylogenetic delineation to increase inference accuracy by 7%.
Development of a new gene assignment method to reduce RAM usage without loss of accuracy.
Achieved a 7% relative increase in orthogroup inference accuracy.
New method significantly decreased overall runtime RAM usage while maintaining inference quality.

Abstract

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 .

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