ArticleBioinformatics (Oxford, England)2017
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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59 citing papers in PubMed, 115 citations in OpenAlex.
- An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection.Nature immunology · 2026Article
- OMAnnotator: a novel approach to building an annotated consensus genome sequence.Bioinformatics advances · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- A multi-omic characterization of the physiological responses to salt stress in Scenedesmus obliquus UTEX393.Communications biology · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Annotation matters: the effect of structural gene annotation on orthology inference.Bioinformatics (Oxford, England) · 2025Article
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- Cretaceous amber inclusions illuminate the evolutionary origin of tardigrades.Communications biology · 2024Article
- Review
- Global gene expression profile and functional analysis reveal the conservation of reproduction-associated gene networks in Gossypium hirsutum.Plant reproduction · 2024Article
- Informatic challenges and advances in illuminating the druggable proteome.Drug discovery today · 2024Review
- Inferring Interaction Networks from Transcriptomic Data: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Leveraging genomic redundancy to improve inference and alignment of orthologous proteins.G3 (Bethesda, Md.) · 2023Article
- Engineering homoeologs provide a fine scale for quantitative traits in polyploid.Plant biotechnology journal · 2023Article
- Phylogenomics reveals the history of host use in mosquitoes.Nature communications · 2023Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- Integrating gene annotation with orthology inference at scale.Science (New York, N.Y.) · 2023Article
- OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.PLoS biology · 2022Article
- Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level.mSystems · 2022Article
- Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico.Journal of molecular evolution · 2022Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAccurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix). Yet substantial challenges remain, in particular in coping with fragmented genes or genes evolving at different rates after duplication, and in scaling to large datasets. With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.
resultsWe present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species paralogs evolving at different rates, and (ii) minimizing errors in the pairwise orthology verification step by testing the consistency of pairwise distance estimates, which can be problematic in the presence of fragmentary sequences. In addition we introduce a more scalable procedure for hierarchical orthologous group (HOG) clustering, which are several orders of magnitude faster on large datasets. Using the Quest for Orthologs consortium orthology benchmark service, we show that these changes translate into substantial improvement on multiple empirical datasets. AVAILABILITY AND IMPLEMENTATION: This new OMA 2.0 algorithm is used in the OMA database ( http://omabrowser.org ) from the March 2017 release onwards, and can be run on custom genomes using OMA standalone version 2.0 and above ( http://omabrowser.org/standalone ). CONTACT: christophe.dessimoz@unil.ch or adrian.altenhoff@inf.ethz.ch.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.