ETE Toolkit 4
Scope
Use ETE 4 to work with an existing tree:
- Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write Newick trees
- Compare topologies and calculate phylogenetic distances
- Find repeated subtree topologies with
TreePattern - Analyze gene trees with
PhyloTree - Query local NCBI or GTDB taxonomy databases
- Explore large trees interactively with SmartView
- Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview
ETE does not replace sequence alignment or phylogenetic inference software. For raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or another inference tool; then load the resulting tree into ETE.
Current Target
This skill targets ETE 4.4.0, released September 3, 2025 and verified as the current PyPI release on July 23, 2026.
Use https://etetoolkit.github.io/ete/ for ETE 4 documentation. The
etetoolkit.org/docs/latest pages are legacy ETE 3 documentation despite the
URL name.
Do not silently translate these examples back to ETE 3:
- Package and import:
ete4, notete3 - File input: pass an open file object; use strings for Newick text and do not rely on path-stri…
