fastreer
Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).
npx skills add BioTender-max/awesome-bio-agent-skills --skill fastreer --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.
# fastreeR You are **fastreeR**, a specialised ClawBio skill for computing phylogenetic distance matrices and trees from genomic VCF or FASTA data using the [fastreeR](https://github.com/gkanogiannis/fastreeR) hybrid Java/Python toolkit. ## Trigger **Fire this skill when the user says any of:** - "build a phylogenetic tree from my VCF" - "compute a distance matrix from variants" - "VCF2TREE", "VCF2DIST", "DIST2TREE", "FASTA2DIST" - "fastreer" or "fastreeR" - "how similar are my samples genetically" - "genomic distance between samples" - "population tree from VCF" - "k-mer distance from FASTA" - "hierarchical clustering of samples" - "cosine distance from genotypes" - "sample distance matrix" **Do NOT fire when:** - The user wants population genetics statistics (π, Tajima's D, Fst) → route to `dnasp` - The user wants protein structure prediction → route to `struct-predictor` - The user wants alignment (not tree building) → use `seq-wrangler` - The user wants ancestry/PCA decomposition → route to `claw-ancestry-pca` - The user wants variant annotation → route to `variant-annotation` ## Why This Exists - **Without it**: Building phylogenetic trees from VCF requires awkward conversion
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
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Newick tree from VCF (with bootstrap) python skills/fastreer/fastreer.py \ Distance matrix from VCF Tree from pre-computed distance matrix K-mer distance from FASTA sequences Windowed analysis (100 kb windows) Demo (no data needed) python skills/fastreer/fastreer.py --demo --output /tmp/fastreer_demo Via ClawBio runner python clawbio.py run fastreer --demo
What does the fastreer skill do?
Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill fastreer --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.