ETE Toolkit: Phylogenetic Tree Analysis and Visualization

ETE Toolkit: Phylogenetic Tree Analysis and Visualization

Overview

ETE Toolkit (ETE3) is a Python framework for phylogenetic tree exploration, manipulation, and publication-quality visualization. It supports reading and writing Newick, NHX, PhyloXML, and NeXML formats, rich node annotation, programmatic tree traversal, NCBI taxonomy integration, and a flexible rendering engine for customizable tree figures. ETE3 is widely used in comparative genomics, phylogenomics, and evolutionary biology workflows.

When to Use

• Parse phylogenetic trees from Newick, NHX, PhyloXML, or NeXML files and programmatically traverse or modify topology
• Annotate tree nodes with metadata (bootstrap values, gene names, taxonomic ranks, expression data) for visualization or downstream analysis
• Render publication-quality tree figures with custom node shapes, colors, branch widths, and face decorations using TreeStyle and NodeStyle
• Map NCBI taxonomy IDs to lineage information, validate species names, or build taxonomy-aware trees
• Compute evolutionary statistics: branch lengths, tree distances (Robinson-Foulds), LCA queries, monophyly tests
• Build PhyloTree objects for comparative genomics — gene duplication/speciation event annotation, orthologs/paralogs inference
• Prune, reroot, or ultrametricize trees programmatically before passing to downstream tools (BEAST, IQ-TREE, etc.)
• For sequence alignment prior to tree building, use biopython-molecular-biology instead

Prerequisites

• Python packages: ete3, numpy, PyQt5 (for interactive rendering), lxml (for PhyloXML)
• Data requirements: Newick string or tree file; NCBI taxonomy database (downloaded on first use for NCBI module)
• Environment: Python 3.6+; PyQt5 required for TreeStyle rendering and interactive GUI; headless rendering requires xvfb

Check before installing: The tool may already be available in the current environment (e.g., inside a pixi / conda env). Run command -v python first and skip the install commands below if it returns a path. When running inside a pixi project, invoke the tool via pixi run python rather than bare python.

pip install ete3 numpy lxml PyQt5
# For headless rendering on Linux servers:
# apt-get install xvfb python3-pyqt5

Quick Start

from ete3 import Tree

# Load a Newick tree and inspect basic properties
t = Tree("((A:0.1,B:0.2)AB:0.3,(C:0.4,D:0.1)CD:0.2)root;")
print(f"Number of leaves: {len(t.get_leaves())}")
print(f"Leaf names: {t.get_leaf_names()}")