Scientific Phylogenetics (ETE Toolkit)

researched 2026-05-25· 0 sources · 8 concepts · skill scientific-pkg-etetoolkit

ETE (Environment for Tree Exploration) is a Python toolkit for phylogenetic and hierarchical tree analysis. Core use cases: tree I/O and manipulation, evolutionary event detection, NCBI taxonomy integ

ETE Toolkit (ete3)

ETE (Environment for Tree Exploration) is a Python toolkit for phylogenetic and hierarchical tree analysis. Core use cases: tree I/O and manipulation, evolutionary event detection, NCBI taxonomy integration, visualization, and clustering analysis. [source]

When to use this skill

Use for: loading/pruning/rerooting/traversing Newick/NHX/PhyloXML trees; detecting evolutionary events (duplication, speciation) and identifying orthologs/paralogs; NCBI taxonomy queries, lineage retrieval, tree annotation; tree visualization (PDF/SVG/PNG) with custom NodeStyle/Faces/layout functions; Robinson-Foulds comparison; ClusterTree heatmaps. [source]
When not to use: generating sequence alignments, running inference tools (IQ-TREE, RAxML), or general bioinformatics not involving tree structures. [source]

Installation

NCBI Taxonomy first-run: NCBITaxa() downloads ~300 MB to ~/.etetoolkit/taxa.sqlite on first instantiation; subsequent calls are fast local lookups. [source]

Tree I/O and basic manipulation

Newick format codes (format= on read/write): 0 = flexible w/ branch lengths (default read); 1 = internal node names; 2 = bootstrap/support; 5 = internal names + branch lengths; 8 = all features; 9 = leaf names only; 100 = topology only. [source]
NHX preserves custom features: [source]

Visualization

Layout function for per-node faces: [source]

Troubleshooting

ModuleNotFoundError: No module named 'ete3' → pip install ete3 [source]
Qt rendering errors (render/show fails) → brew install qt@5 (macOS), apt-get install python3-pyqt5 python3-pyqt5.qtsvg (Ubuntu), or pip install ete3[gui] [source]
NCBI taxonomy DB corrupt/missing → NCBITaxa().update_taxonomy_database() [source]
robinson_foulds shared-leaf error → both trees need same leaf set, or pass unrooted_trees=True [source]
Sources: etetoolkit.org docs (tutorial, reference_tree), pypi.org/project/ete3. [source]

Children

Phylogenetic Tree Manipulation (frontier)
Evolutionary Event Detection (frontier)
NCBI Taxonomy Integration (frontier)
Tree Visualization (frontier)

Frontier under this node: Evolutionary Event Detection, NCBI Taxonomy Integration, Phylogenetic Tree Manipulation, Tree Visualization

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