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bio-comparative-genomics-ortholog-inference

Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplicati

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Atualizado há 4 meses

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Version Compatibility

Reference examples tested with: OrthoFinder 3.0+ (bioRxiv 2025.07.15.664860), SonicParanoid 2.0.8+ (Cosentino 2023), Broccoli 1.2+ (Derelle 2020), ProteinOrtho 6.3.0+ (Lechner 2011 + recent), OMA standalone 2.6.0+, FastOMA 0.3.5+ (Majidian 2025), eggNOG-mapper 2.1.12+, JustOrthologs 2.0+, DIAMOND 2.1.10+, MMseqs2 17-b804f+, IQ-TREE 2.3.6+, BUSCO 5.7+, Compleasm 0.2.7+, BioPython 1.84+, R 4.4+ for downstream tree-based reconciliation.

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