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Orthology inference at scale with FastOMA

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Majidian, Sina, Nevers, Yannis, Yazdizadeh Kharrazi, Ali, Warwick Vesztrocy, Alex, Pascarelli, Stefano, Moi, David, Glover, Natasha, Altenhoff, Adrian M. +1 more·2025·Nature Methods
DOI 10.1038/s41592-024-02552-8PMC PMC11810774

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Abstract

The surge in genome data, with ongoing efforts aiming to sequence 1.5 M eukaryotes in a decade, could revolutionize genomics, revealing the origins, evolution and genetic innovations of biological processes. Yet, traditional genomics methods scale poorly with such large datasets. Here, addressing this, ‘FastOMA’ provides linear scalability for orthology inference, enabling the processing of thousands of eukaryotic genomes within a day. FastOMA maintains the high accuracy and resolution of the well-established Orthologous Matrix (OMA) approach in benchmarks. FastOMA is available via GitHub at https://github.com/DessimozLab/FastOMA/ .

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Cited by

Sorted by citations

Authors
Majidian, S., Nevers, Y., Yazdizadeh Kharrazi, A., Warwick Vesztrocy, A., Pascarelli, S., Moi, D., Glover, N., Altenhoff, A. M., & Dessimoz, C.
Affiliations
SIB Swiss Institute of Bioinformatics (CH)
Corresponding author
Dessimoz, Christophe
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2025-01-03
Volume
22
Issue
2
Pages
269-272
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/s41592-024-02552-8
PMC
PMC11810774
OpenAlex
W4406034714
Cited by
30
References
2
Citations by year
2026: 15 · 2025: 12 · 2024: 3
FWCI
7.46
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Methods (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • SERVAL (Université de Lausanne) (acceptedVersion, cc-by)
  • IRIS (submittedVersion, cc-by)
  • Chalmers Research (Chalmers University of Technology) (submittedVersion, cc-by)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
  • ETH Zürich Research Collection
Funders
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (205085)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
orthology inference, eukaryotic genomes, linear scalability, protein evolution
MeSH terms
Algorithms, Humans, Software, Genome, Computational Biology, Genomics

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