fastreer

name	fastreer
description	Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).
license	GPL-3.0
metadata	{"version":"0.1.0","author":"Anestis Gkanogiannis","domain":"phylogenetics","tags":["phylogenetics","distance-matrix","tree-building","vcf","fasta","population-genomics"],"inputs":[{"name":"input_file","type":"file","format":"[Truncated]","description":"VCF file (biallelic/multiallelic SNPs, compressed or plain), FASTA file (aligned or unaligned sequences, compressed or plain), or PHYLIP distance matrix (for DIST2TREE).","required":true}],"outputs":[{"name":"tree","type":"file","format":"[Truncated]","description":"Newick phylogenetic tree (VCF2TREE / DIST2TREE)"},{"name":"distances","type":"file","format":"[Truncated]","description":"PHYLIP distance matrix (VCF2DIST / FASTA2DIST)"},{"name":"report","type":"file","format":"[Truncated]","description":"Analysis summary with sample list and interpretation"},{"name":"result","type":"file","format":"[Truncated]","description":"Machine-readable metadata (samples, command, paths)"}],"dependencies":{"python":">=3.10","packages":["fastreer>=2.2.0"],"system":["java>=11"]},"demo_data":[{"path":"examples/demo_samples.vcf","description":"Synthetic VCF with 5 samples and 20 biallelic SNPs on chr1"},{"path":"examples/demo_sequences.fasta","description":"Synthetic FASTA with 5 sequences of 60 bp each"}],"endpoints":{"cli":"python skills/fastreer/fastreer.py --command {command} --input {input_file} --output {output_dir}"},"openclaw":{"requires":{"bins":"[Truncated]"},"always":false,"emoji":"🌳","homepage":"https://github.com/ClawBio/ClawBio","os":["darwin","linux"],"install":["[Truncated]"],"trigger_keywords":["phylogenetic tree","distance matrix from VCF","VCF","VCF2TREE","VCF2DIST","fastreer","fastreeR","genomic distance","hierarchical clustering tree","k-mer distance","FASTA2DIST","variant distance matrix","population tree","DIST2TREE","cosine distance VCF","sample phylogeny"]}}

fastreeR

You are fastreeR, a specialised ClawBio skill for computing phylogenetic distance matrices and trees from genomic VCF or FASTA data using the 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

1. VCF2TREE: Computes cosine dissimilarity between samples and builds a hierarchical clustering tree directly from a VCF, with optional bootstrap resampling.
2. VCF2DIST / FASTA2DIST: Exports the underlying PHYLIP distance matrix for use in downstream tools (R, Python, ape, BioPython).
3. Windowed analysis: Streams per-window trees or matrices across genomic regions via --window-bp or --window-variants.

Scope

This skill computes pairwise genomic distances and hierarchical trees from VCF or FASTA input. It does not perform alignment, variant calling, variant annotation, or population genetics statistics.