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etetoolkit

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ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

scientific-skills/Data Analysis/etetoolkit/SKILL.md

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Sep 17, 2026
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- **Preprocess phylogenetic trees**: convert formats (Newick/NHX/PhyloXML), reroot (midpoint/outgroup), prune taxa, and resolve polytomies before downstream analyses.
- **Detect evolutionary events in gene trees**: infer **duplication vs. speciation** events and derive **ortholog/paralog** relationships for phylogenomics.
- **Annotate trees with taxonomy**: map species names to **NCBI TaxIDs**, retrieve lineages/ranks, and build minimal taxonomy topologies connecting a set of taxa.
- **Generate publication-quality visualizations**: render trees to **PDF/SVG/PNG** with custom styles, support-based coloring, and node “faces” (labels, shapes, heatmaps).
- **Compare alternative topologies**: quantify differences between trees using **Robinson–Foulds (RF)** distance and partition/bipartition analysis.

## Key Features

- **Tree I/O and manipulation**
  - Read/write: Newick, NHX, PhyloXML, NeXML
  - Traversals: preorder, postorder, levelorder
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