# Fastreer

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Engineering
- License: GPL-3.0
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill fastreer -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill fastreer -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill fastreer -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill fastreer -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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 steps
  (VCF → PLINK → distance matrix → external tree software) with no unified output.
- **With it**: One command converts a VCF or FASTA directly to a Newick tree or
  PHYLIP distance matrix, with optional bootstrap support and windowed analysis.
- **Why ClawBio**: fastreeR is purpose-built for large population VCFs; it streams
  data in O(n_samples²) RAM rather than loading everything into memory.

## Core Capabilities

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/fastreer/SKILL.md