Alterlab etetoolkit

Skill AlterLab-IEU/AlterLab-Academic-Skills/skills/bioinformatics/alterlab-etetoolkit

239 evaluated academic Claude/agent skills across 17 research domains (bioinformatics, data science, clinical, social-science methods, Turkish academia & more). Executable eval per skill, deterministic citation verifier, research→write→review→publish pipeline, and a skill-finder front door. Claude Code, Cursor, Codex, Gemini CLI & Copilot.

Install

npx -y skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-etetoolkit

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What its author says it does

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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.

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SKILL.md

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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).

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

Core Workflow

The canonical minimal pattern — load, edit, save:

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, Faces, 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.