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Scikitbio tree comparison starter

Skill ma-compbio-lab/SkillFoundry/skills/ecology-evolution-and-biodiversity/scikitbio-tree-comparison-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill scikitbio-tree-comparison-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.1 KB, 252 tokens by cl100k_base, as published. Nobody here has run it

scikit-bio Tree Comparison Starter

Use this skill to parse two small Newick trees with scikit-bio and summarize a compact topology-comparison result.

What it does

  • Parses two deterministic toy phylogenies from Newick strings.
  • Summarizes tip labels, total branch lengths, and both unweighted and weighted Robinson-Foulds distances.
  • Returns a small JSON payload suitable for smoke tests and future phylogenetic workflow extensions.

When to use it

  • You need a runnable starter for Phylogenetic comparative workflows.
  • You want a lightweight verified tree-comparison example before larger comparative biology analyses.

Example

slurm/envs/ecology/bin/python skills/ecology-evolution-and-biodiversity/scikitbio-tree-comparison-starter/scripts/run_scikitbio_tree_comparison.py \
  --out scratch/ecology/tree_comparison_summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/ecology-evolution-and-biodiversity/scikitbio-tree-comparison-starter/tests -p 'test_*.py'
  • Repository smoke: python3 -m unittest tests.smoke.test_phase31_frontier_leaf_conversion_skills -v

Keep looking

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