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.

ete3 or ete4?

The examples in this skill and its references are written for ete3 3.1.3, which is still what most published pipelines import — but ete3 has had no release since May 2023, and ete4 (4.4.0, Sept 2025) is the maintained line. Port deliberately: the ete4 API is not drop-in.

ete3	ete4
from ete3 import Tree	from ete4 import Tree
Tree("t.nw", format=1)	Tree(open("t.nw"), parser=1) — the keyword is parser
tree.iter_leaves() / get_leaves()	tree.leaves()
custom features via node.add_feature()	node.props[...] dictionary
Qt-based show() / render() (needs PyQt5)	browser-based explore() with adaptive zoom, plus GTDB taxonomy support

Check which one is installed before writing code (python -c "import ete4"), and say which you targeted in the methods.

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:

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.

Does NOT Trigger

Scenario	Use Instead
Build a tree from unaligned sequences (align + model selection + ML inference)	alterlab-phylogenetics
Distance matrices, diversity metrics, or ordination from alignments	alterlab-scikit-bio
Tree I/O inside a broader Biopython pipeline (Bio.Phylo)	alterlab-biopython
Generic graph algorithms on a non-tree network	alterlab-networkx
Taxonomic classification of amplicon reads	alterlab-qiime2-amplicon

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.

Part of the AlterLab Academic Skills suite.