etetoolkitlisted

# 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`, not `ete3` - File input: pass an open file object; use strings for Newick text and do not rely on path-string heuristics retained in ETE 4.4.0 - Newick selection: `parser=`, not `format=` - Node metadata: `props`, `add_prop()`, and `add_props()` - Iteration: `leaves()`, `descendants()`, and related methods return iterators - Predicates: `node.is_leaf` and `node.is_root` are properties, not methods - Node