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name: 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 in skbio.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.