executing-plans
executing-plans
Use when executing an implementation plan in the current session as the implementer yourself — your human partner chose inline execution, or no subagent tool is available
Explorer les Skills
Productivité · SKILL.md
trees-phylogeny
trees-phylogenyUse scikit-bio TreeNode objects, Newick trees, distance-based tree construction, tree comparison, consensus, and phylogenetic tree constraints for downstream diversity analyses.
Independent GitHub snapshot · Automated classification · Original documentation governs
Documentation de la Skill
GitHubname: trees-phylogeny description: "Use scikit-bio TreeNode objects, Newick trees, distance-based tree construction, tree comparison, consensus, and phylogenetic tree constraints for downstream diversity analyses." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause
trees-phylogeny
Use this sub-skill when an agent needs to read or write Newick, navigate or edit a TreeNode, build a phylogeny from a DistanceMatrix, compare tree topology or branch lengths, build a majority-rule consensus, or prepare a tree/taxa set for Faith PD or UniFrac.
Quick Routing
| Need | Start here |
|---|---|
| Parse Newick, inspect tips, traverse nodes, root or reroot | API reference and workflows |
| Keep or remove taxa, prune empty internals, repair polytomies | workflows |
| Construct a tree from pairwise distances | workflows |
| Improve a candidate tree with NNI | API reference |
| Compare tree topology or branch lengths | workflows |
| Derive a majority-rule consensus | workflows |
| Fix errors before Faith PD or UniFrac | troubleshooting |
Boundaries
- This sub-skill covers
skbio.TreeNode/skbio.tree.TreeNode, tree algorithms inskbio.tree, and tree/taxa constraints needed by phylogenetic diversity metrics. - For distance matrix statistics, PERMANOVA/PERMDisp/ANOSIM, and ordination from distance matrices, use
../statistics-ordination/SKILL.md. - For actually running alpha/beta diversity metrics such as Faith PD or UniFrac, use
../diversity-tables/SKILL.md; this sub-skill only prepares and diagnoses the tree and taxa inputs. - For sequence alignment or sequence-derived distances before tree construction, use
../sequences-alignment/SKILL.md.
Public Smoke Check
Run the bundled script from any working directory after installing scikit-bio:
python scripts/tree_phylogeny_smoke.py
python scripts/tree_phylogeny_smoke.py --algorithm upgma
python scripts/tree_phylogeny_smoke.py --help
The script parses a small Newick tree, validates rooted/tip/branch-length expectations, builds a DistanceMatrix, runs nj or upgma, and prints compact JSON. It imports public scikit-bio APIs only.