ArticleGenome biology and evolution2020
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench.
Article in Genome biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Discovering New Orthologous Groups with P-COGs.Biochemical genetics · 2026Article
- A comparative approach for selecting orthologous candidate genes in genome-wide association studies across multiple species.Plant physiology · 2026Article
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- Genome architecture reveals hidden strain-level diversity in the highly conserved fish pathogen Nocardia seriolae.Access microbiology · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- A curated benchmark dataset for molecular identification based on genome skimming.Scientific data · 2025Article
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- Genome assembly and population analysis of tetraploid marama bean reveal two distinct genome types.Scientific reports · 2025Article
- SCARAP: scalable cross-species comparative genomics of prokaryotes.Bioinformatics (Oxford, England) · 2024Article
- SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.Genome biology · 2024Article
- Evolutionary Study of Protein Short Tandem Repeats in Protein Families.Biomolecules · 2023Article
- Fixed Allele Differences Associated With the Centromere Reveal Chromosome Morphology and Rearrangements in a Reptile (Varanus acanthurus BOULENGER).Molecular biology and evolution · 2023Article
- OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity.Nucleic acids research · 2023Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- The genomic basis of host and vector specificity in non-pathogenic trypanosomatids.Biology open · 2022Article
- SHOOT: phylogenetic gene search and ortholog inference.Genome biology · 2022Article
- Evolution of chlorophyll degradation is associated with plant transition to land.The Plant journal : for cell and molecular biology · 2022Article
- Orthology Clusters from Gene Trees with Possvm.Molecular biology and evolution · 2021Article
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2 authors.
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Abstract
Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert-curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup inference. Here, we leveraged improvements in tree inference algorithms and computational resources to reinterrogate these RefOGs and carry out an extensive phylogenetic delineation of their composition. This phylogenetic revision altered the membership of 31 of the 70 RefOGs, with 24 subject to extensive revision and 7 that required minor changes. We further used these revised and updated RefOGs to provide an assessment of the orthogroup inference accuracy of widely used orthogroup inference methods. Finally, we provide an open-source benchmarking suite to support the future development and use of the Orthobench benchmark.
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