ArticleBioinformatics (Oxford, England)2022
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- High-level polymyxin B resistance and underlying mechanism in a multidrug-resistant Acinetobacter strain isolated from the marine plastisphere.The Journal of antibiotics · 2026Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- AmDB: functional genomics database of Astragalus membranaceus.BMC genomics · 2025Article
- Uukuniemi virus infection causes a pervasive remodelling of the RNA-binding proteome in tick cells.PLoS pathogens · 2025Article
- Ethylene response factors as potential regulators of cell wall formation in celery (Apium graveolens L.) collenchyma: phylogeny and gene expression analysis.Protoplasma · 2025Article
- Feature Architecture-Aware Ortholog Search With fDOG Reveals the Distribution of Plant Cell Wall-Degrading Enzymes Across Life.Molecular biology and evolution · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- Unearthing the secrets of Australia's most enigmatic and cryptic mammal, the marsupial mole.Science advances · 2025Article
- DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs.Bioinformatics (Oxford, England) · 2024Article
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- PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters.Nucleic acids research · 2024Article
- Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RpoS-Regulated Genes and Phenotypes in the Phytopathogenic BacteriumInternational journal of molecular sciences · 2023Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
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- RoseAP: an analytical platform for gene function ofFrontiers in plant science · 2023Article
- PlantCHRs: A comprehensive database of plant chromatin remodeling factors.Computational and structural biotechnology journal · 2023Article
- Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set.Applications in plant sciencesArticle
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2 authors.
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Abstract
summaryPredicting orthologs, genes in different species having shared ancestry, is an important task in bioinformatics. Orthology prediction tools are required to make accurate and fast predictions, in order to analyze large amounts of data within a feasible time frame. InParanoid is a well-known algorithm for orthology analysis, shown to perform well in benchmarks, but having the major limitation of long runtimes on large datasets. Here, we present an update to the InParanoid algorithm that can use the faster tool DIAMOND instead of BLAST for the homolog search step. We show that it reduces the runtime by 94%, while still obtaining similar performance in the Quest for Orthologs benchmark. AVAILABILITY AND IMPLEMENTATION: The source code is available at (https://bitbucket.org/sonnhammergroup/inparanoid). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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