Generate phylogenetic trees and distance matrices from VCF or FASTA genomic data.
npx skills add https://github.com/ClawBio/ClawBio --skill fastreer
Please help me install this Agent Skill. Skill: fastreer Source: https://github.com/ClawBio/ClawBio/tree/main/skills/fastreer Command: npx skills add https://github.com/ClawBio/ClawBio --skill fastreer
Building phylogenetic trees from genomic variant data normally requires awkward multi-step conversions (VCF to PLINK to distance matrix to external tree software) with no unified output. This Skill converts a VCF or FASTA file directly into a Newick tree or PHYLIP distance matrix in one command, with optional bootstrap support and windowed analysis.
Ask the agent to build a phylogenetic tree from your VCF file, or run the built-in demo with "run the fastreer demo" to see the expected output on synthetic data.
High-intent search queries and answers about installing and using this skill.
Run the VCF2TREE command with your VCF as input; it computes cosine dissimilarity between samples from genotype dosages and applies UPGMA hierarchical clustering to produce a Newick tree. Bootstrap support can be added with the bootstrap flag.
Use the FASTA2DIST command, which computes D2S k-mer distances between sequences without requiring alignment. The default k-mer size is 4, adjustable between 3 and 8, and output is a PHYLIP distance matrix.
Yes, fastreeR is a hybrid Java/Python toolkit and requires Java 11 or later in addition to the fastreer Python package. The skill checks for both before running and exits with a clear error if either is missing.
The default JVM heap of 256 MB is insufficient for more than about 500 samples. Increase the memory flag following the rule of roughly 4 times n_samples squared times threads divided by one million MB.
The VCF must contain GT genotype fields and at least one sample column; variant-only VCFs silently fail. The skill does not perform alignment, variant calling, annotation, or population genetics statistics like Fst or Tajima's D.
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MubasherMohammedAnalyze population genetic structure with PCA against SGDP data.
roeimed0Build and compare phylogenetic trees from sequence alignments using distance-based, maximum-likelihood, and Bayesian methods.
