Alterlab Etetoolkit

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.

1. Phylogenetic analysis — alignment linkage, species naming, duplication/speciation

detection (Species Overlap or reconciliation), orthology/paralogy.

1. NCBI Taxonomy — local cached DB, taxid↔name translation, lineage retrieval,

taxonomy-tree building, tree annotation.

1. Visualization — PNG/PDF/SVG export, rectangular/circular layouts, NodeStyle,

Face objects, layout functions, interactive GUI.

1. Clustering analysis — ClusterTree, data-matrix linking, silhouette/Dunn metrics,

heatmap views.

1. 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.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: AlterLab-IEU
• Source: AlterLab-IEU/AlterLab-Academic-Skills
• License: MIT
• Homepage: https://alterlab-ieu.github.io/AlterLab-Academic-Skills/

Install and usage instructions live in the source repository linked above.