etetoolkit

1# ETE Toolkit 4
2 
3## Scope
4 
5Use ETE 4 to work with an existing tree:
6 
7- Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write
8  Newick trees
9- Compare topologies and calculate phylogenetic distances
10- Find repeated subtree topologies with `TreePattern`
11- Analyze gene trees with `PhyloTree`
12- Query local NCBI or GTDB taxonomy databases
13- Explore large trees interactively with SmartView
14- Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview
15 
16ETE does not replace sequence alignment or phylogenetic inference software. For
17raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or
18another inference tool; then load the resulting tree into ETE.
19 
20## Current Target
21 
22This skill targets **ETE 4.4.0**, released September 3, 2025 and verified as the
23current PyPI release on September 30, 2026.
24Core, phylogeny, local synthetic taxonomy and helper checks target this released
25package, not unreleased upstream changes. See
26[`references/review.md`](references/review.md) for executed coverage and limitations.
27 
28Use `https://etetoolkit.github.io/ete/` for ETE 4 documentation. The
29`etetoolkit.org/docs/latest` pages are legacy ETE 3 documentation despite the
30URL name.
31 
32Do not silently translate these examples back to ETE 3:
33 
34- Package and import: `ete4`, not `ete3`
35- File input: pass an open file object; use strings for Newick text and do not
36  rely on path-string heuristics retained in ETE 4.4.0
37- Newick selection: `parser=`, not `format=`
38…