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