ArticleGenome biology2024
SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.Molecular biology and evolution · 2026Article
- Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms.Molecular systems biology · 2026Article
- Article
- Discovering New Orthologous Groups with P-COGs.Biochemical genetics · 2026Article
- Convergent genomic trajectories shape adaptation to life on land across animal lineages.Nature communications · 2026Article
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- A programmableApplied and environmental microbiology · 2026Article
- LSGFA: domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference.BMC bioinformatics · 2026Article
- Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus.Scientific reports · 2026Article
- BINge: Multispecies Ortholog Clustering for Differential Gene Expression Analyses.Molecular ecology resources · 2026Article
- DIOPT: the DRSC Integrative Ortholog Prediction Tool, 2026 update.bioRxiv : the preprint server for biology · 2026Article
- Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Improved genome assembly of whale shark, the world's biggest fish: revealing intragenomic heterogeneity in molecular evolution.GigaScience · 2026Article
- Whole genome analysis of toxic Papilionidae butterflies utilizing aristolochic acid, Pachliopta aristolochiae, and Byasa alcinous.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity.Journal of molecular evolution · 2025Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- 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
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- Convergent losses of arbuscular mycorrhizal symbiosis in carnivorous plants.The New phytologist · 2025Article
- Genomic Features Underlying the Origin of Sociality and the Diversification of Caste Systems in Termites.Molecular biology and evolution · 2025Article
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3 authors.
Funding
Abstract
Accurate inference of orthologous genes constitutes a prerequisite for comparative and evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; however, its scalability and accuracy have been hampered by time-consuming all-versus-all alignments and the existence of proteins with complex domain architectures. Here, we present a substantial update of SonicParanoid, where a gradient boosting predictor halves the execution time and a language model doubles the recall. Application to empirical large-scale and standardized benchmark datasets shows that SonicParanoid2 is much faster than comparable methods and also the most accurate. SonicParanoid2 is available at https://gitlab.com/salvo981/sonicparanoid2 and https://zenodo.org/doi/10.5281/zenodo.11371108 .
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