Agent skill · research science · k-dense-ai
etetoolkit
Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.
Why this skill is useful
Provides specific commands and patterns for manipulating phylogenetic trees that the AI wouldn't reliably generate on its own.
What it needs
Requires ete4 installed locally. About 6k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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, addprop(), and addprops() Iteration: leaves(), descendants(), and related methods return iterators Predicates: node.isleaf and node.isroot are properties, not methods Node lookup: tree["name"], not tree & "name" For porting older code, load references/migration-ete3-to-ete4.md. Installation Install the pinned base package: Add only the visualization extra required by the workflow: Confirm the active environment: No credentials are required. NCBI and GTDB workflows download public taxonomy data and can consume substantial disk space; see references/taxonomy.md before the first update. Quick Start Choose the parser deliberately. A parser mismatch is the most common cause of NewickError, lost internal labels, or support values being read as names. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/etetoolkit