bio-protein-clustering-pangenome
Cluster proteins into orthogroups and derive pangenome matrices.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-protein-clustering-pangenome --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bio Protein Clustering Pangenome Cluster proteins into orthogroups and derive pangenome matrices. ## Instructions 1. Cluster proteins. Choose the tool by dataset size and goal: - Default for orthology inference up to a few hundred genomes: **OrthoFinder v3** (improved accuracy and lower RAM at scale, supports MSA-based gene trees; supersedes OrthoFinder v2 and OrthoMCL workflows). - Very large pangenomes where OrthoFinder is too RAM-heavy: **ProteinOrtho v6.1.7+** as the fast, scalable alternative. - Sequence clustering (not strict orthology) and similarity search backbones: **MMseqs2** v15-6f452+. Enable GPU mode (`mmseqs ... --gpu`) on CUDA Turing+ nodes for a ~20× speedup at near-identical sensitivity. 2. Build presence/absence matrix AND an integer copy-number matrix (orthogroup × genome) covering the query AND the close relatives produced by `/bio-phylogenomics`. 3. Compute core/accessory/cloud/singleton partitions. 4. Identify single-copy orthologs for phylogenetic analysis. 5. Discriminate paralogs from orthologs in multi-copy gene families. 6. Calculate pangenome statistics (completeness, orthogroup occupancy). 7. When a query genome or genome set is under study, use the
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-protein-clustering-pangenome skill do?
Cluster proteins into orthogroups and derive pangenome matrices.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-protein-clustering-pangenome --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.