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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 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

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill comparative-genomics__ortholog-inference --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 3
SKILL.md size: 33 KB
Bundled scripts: yes
Path: skills/bioskills/comparative-genomics__ortholog-inference/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## 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. Before using code patterns, verify installed versions match. If versions differ: - CLI: `orthofinder --help`; `sonicparanoid --help`; `oma --help` - Python: `pip show eggnog-mapper`; `which fastoma` If code throws `Diamond requires N more sequences than provided`, `KeyError on species tree taxa`, `STAG branch length 0`, or `HOG file format mismatch`, the OrthoFinder v2 -> v3 file layout changed (Orthogroups/ -> Phylogenetic_Hierarchical_Orthogroups/; rooted gene trees are now per-HOG); update parsing accordingly. # Ortholog Inference **"Find the orthologs of my gene(s) across these species"** -> Choose between graph-based (RBH / similarity-clustering: fast, lower recall) and tree-based (gene-tree reconciliation: higher accuracy

What's inside
Steps it walks through
  1. Version Compatibility
  2. Algorithmic Taxonomy
  3. Decision Tree by Experimental Scenario
  4. Per-Method Failure Modes
  5. Hidden paralogy from missing outgroup
  6. Splice isoforms inflating copy number
  7. Annotation heterogeneity inflating lineage-specific OGs
  8. Ortholog conjecture violations
  9. RBH symmetric-but-wrong errors
  10. Synteny ignored in WGD lineages
  11. MAFFT-only alignment in OrthoFinder MSA mode
  12. Quantitative Thresholds
  13. OrthoFinder3 Standard Workflow
  14. SonicParanoid2 + Cross-Validation
Ships with 2 files
  • examples/ortholog_analysis.py
  • usage-guide.md
Commands it runs
Pre-clean proteomes: longest isoform per gene
for f in raw_proteomes/*.faa; do
python tools/primary_transcript.py $f > cleaned/$(basename $f)
done
OrthoFinder v3 with MSA + IQ-TREE for tree-based HOG inference
orthofinder \
Output of interest (v3 layout):
sonicparanoid -i cleaned/ -o sp2_run --mode default --threads 16 --pfam pre-computed
After Cactus alignment producing reference-query chain files
toga.py \
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About this skill
What does the bio-comparative-genomics-ortholog-inference skill do?

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

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill comparative-genomics__ortholog-inference --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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