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Peer-reviewedCC BYNature Methods

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability

  • David Emms1
  • Yi Liu1
  • Laurence J. Belcher1
  • Jonathan Holmes1
  • Steven L. Kelly2
  1. 1Department of Biology, University of Oxford, Oxford, UK
  2. 2Department of Biology, University of Oxford, Oxford, UK. [email protected]
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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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Cite

BibTeXRIS
BibTeX
@article{emms2026orthofinder,
  title = {{OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability}},
  author = {David Emms and Yi Liu and Laurence J. Belcher and Jonathan Holmes and Steven L. Kelly},
  journal = {Nature Methods},
  year = {2026},
  month = jun,
  doi = {10.1038/s41592-026-03126-6},
  url = {https://doi.org/10.1038/s41592-026-03126-6},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability
AU  - David Emms
AU  - Yi Liu
AU  - Laurence J. Belcher
AU  - Jonathan Holmes
AU  - Steven L. Kelly
PY  - 2026
DA  - 2026/06/09
JO  - Nature Methods
DO  - 10.1038/s41592-026-03126-6
UR  - https://doi.org/10.1038/s41592-026-03126-6
AB  - 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 .
SN  - 1548-7091
SN  - 1548-7105
ER  -