bio-comparative-genomics-ortholog-inference
bio-comparative-genomics-ortholog-inference is a Bioinformatics & life sciences skill for AI agents, published by BioTender-max in the awesome-bio-agent-skills repository on GitHub. Skillspace rates bio-comparative-genomics-ortholog-inference C (79/100) and it passed the safety scan; the rating is based on static analysis only.
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 duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.
- Grade
- C
- Quality
- 79 / 100
- Safety
- Passed
- GitHub stars
- 115
Unproven: rated by static analysis only, not yet compared head-to-head.
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Our review
- Architecture
- 97 / 100
- Maturity
- Structured: ships references or scripts
- Security scan
- No issues found
- License
- Not declared. Check the repository before reusing it.
- Adoption
- Adopted by 0 other repositories, in 2 collections
Not checked yet
- Not judged on the rubric yet (not a contender in its category)
- No blind task eval yet
- Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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