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bioRxiv · 10.1101/2025.07.15.664860

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

Emms, D. M.·Liu, Y.·Belcher, L. J.·Holmes, J.·Kelly, S.
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Abstract

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinders 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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Emms, D. M., Liu, Y., Belcher, L. J., Holmes, J., Kelly, S.. 2025-07-16. OrthoFinder: scalable phylogenetic orthology inference for comparative genomics. https://doi.org/10.1101/2025.07.15.664860

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