scikitbio-tree-comparison-starter

Name: scikitbio-tree-comparison-starter
Author: ma-compbio-lab

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How to install scikitbio-tree-comparison-starter?

ma-compbio-lab/skillfoundry/scikitbio-tree-comparison-starter

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

Installs into the current project.

Summary

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

Files · 1

SKILL.md

1	# scikit-bio Tree Comparison Starter
2
3	Use this skill to parse two small Newick trees with `scikit-bio` and summarize a compact topology-comparison result.
4
5	## What it does
6
7	- Parses two deterministic toy phylogenies from Newick strings.
8	- Summarizes tip labels, total branch lengths, and both unweighted and weighted Robinson-Foulds distances.
9	- Returns a small JSON payload suitable for smoke tests and future phylogenetic workflow extensions.
10
11	## When to use it
12
13	- You need a runnable starter for `Phylogenetic comparative workflows`.
14	- You want a lightweight verified tree-comparison example before larger comparative biology analyses.
15
16	## Example
17
18	```bash
19	slurm/envs/ecology/bin/python skills/ecology-evolution-and-biodiversity/scikitbio-tree-comparison-starter/scripts/run_scikitbio_tree_comparison.py \
20	--out scratch/ecology/tree_comparison_summary.json
21	```
22
23	## Verification
24
25	- Skill-local tests: `python3 -m unittest discover -s skills/ecology-evolution-and-biodiversity/scikitbio-tree-comparison-starter/tests -p 'test_*.py'`
26	- Repository smoke: `python3 -m unittest tests.smoke.test_phase31_frontier_leaf_conversion_skills -v`

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