alterlab-etetoolkit

$npx mdskill add AlterLab-IEU/AlterLab-Academic-Skills/alterlab-etetoolkit

Manipulate, annotate, and render phylogenetic trees using ETE Toolkit.

  • Parse, traverse, and reformat Newick/NHX tree files.
  • Runs under uv run python with ete3 package installed.
  • Detects duplication/speciation events to infer orthology and paralogy.
  • Exports publication-quality PDF/SVG figures and queries NCBI taxonomy.

SKILL.md

.github/skills/alterlab-etetoolkitView on GitHub ↗
---
name: alterlab-etetoolkit
description: Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting tree files, doing phylogenomic comparative analysis, or producing publication tree graphics in Python. Part of the AlterLab Academic Skills suite.
license: GPL-3.0
allowed-tools: Read Write Edit Bash(python:*) Bash(uv:*)
compatibility: "Self-contained — runs under `uv run python` with the skill's Python package installed; no API key or account required."
metadata:
    skill-author: AlterLab
    version: "1.0.0"
---

# ETE Toolkit Skill

## Overview

ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical
tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and
integrate with biological databases for phylogenomic research and clustering analysis.

## When to Use

- Parsing, traversing, or reformatting tree files (Newick / NHX / PhyloXML / NeXML)
- Pruning, rooting, collapsing, or resolving polytomies in a tree
- Detecting duplication/speciation events and inferring orthologs/paralogs from gene trees
- Querying NCBI Taxonomy (taxid/name translation, lineages, taxonomy trees)
- Producing publication-quality PDF/SVG/PNG tree figures
- Comparing trees (Robinson-Foulds) or analyzing clustering dendrograms

## Core Capabilities

ETE exposes six capability areas. Each has detailed, copy-ready code in the references
(see Index below).

1. **Tree manipulation** — I/O across formats, traversal (pre/post/levelorder), topology
   edits (prune, root, collapse), distances, RF tree comparison.
2. **Phylogenetic analysis** — alignment linkage, species naming, duplication/speciation
   detection (Species Overlap or reconciliation), orthology/paralogy.
3. **NCBI Taxonomy** — local cached DB, taxid↔name translation, lineage retrieval,
   taxonomy-tree building, tree annotation.
4. **Visualization** — PNG/PDF/SVG export, rectangular/circular layouts, `NodeStyle`,
   `Face` objects, layout functions, interactive GUI.
5. **Clustering analysis** — `ClusterTree`, data-matrix linking, silhouette/Dunn metrics,
   heatmap views.
6. **Tree comparison** — Robinson-Foulds (raw + normalized), partition/bipartition analysis,
   batch pairwise distance matrices.

## Core Workflow

The canonical minimal pattern — load, edit, save:

```python
from ete3 import Tree

# Load tree from file (format 1 = with internal node names)
tree = Tree("tree.nw", format=1)

# Prune to taxa of interest, preserving branch lengths
tree.prune(["species1", "species2", "species3"], preserve_branch_length=True)

# Midpoint root
tree.set_outgroup(tree.get_midpoint_outgroup())

# Save
tree.write(outfile="rooted_tree.nw")
```

For class selection: use `Tree`/`TreeNode` for generic topology work, `PhyloTree` for gene
trees and evolutionary analysis, `ClusterTree` for dendrograms with data matrices, and
`NCBITaxa` for taxonomy queries.

## Command-Line Scripts

- `scripts/tree_operations.py` — stats, format conversion, rerooting, pruning, ASCII view.
  Example: `python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint`
- `scripts/quick_visualize.py` — rapid PDF/PNG rendering with circular layout, support
  coloring, and DPI control. Example:
  `python scripts/quick_visualize.py tree.nw out.pdf --mode c --color-by-support`

## Reference Index

Load the relevant file when detailed information is needed:

- **`references/api_reference.md`** — Complete API for all ETE classes/methods (`Tree`,
  `PhyloTree`, `ClusterTree`, `NCBITaxa`): parameters, return types, code examples.
- **`references/workflows.md`** — Per-task workflow patterns (tree operations, phylogenetic
  analysis, comparison, taxonomy integration, clustering).
- **`references/visualization.md`** — Full visualization guide: `TreeStyle`, `NodeStyle`,
  `Face`s, layout functions, advanced rendering.
- **`references/use_cases.md`** — End-to-end worked use cases (phylogenomic pipeline, batch
  preprocessing, publication figures, automated multi-tree analysis).
- **`references/setup_and_troubleshooting.md`** — Installation, NCBI Taxonomy first-run
  setup, and troubleshooting (imports, Qt rendering, memory, DB corruption).
- **`references/newick_and_best_practices.md`** — Newick/NHX format specifications (0-100)
  and best-practice checklist.

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