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ET
etetoolkit
Maintainer K-Dense Inc. · Last updated April 1, 2026
ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analy.
Original source
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/etetoolkit
- Maintainer
- K-Dense Inc.
- License
- GPL-3.0 license
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.
- tree = Tree("tree.nw", format=1).
Source Doc
Excerpt From SKILL.md
1. Tree Manipulation and Analysis
Load, manipulate, and analyze hierarchical tree structures with support for:
- Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
- Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
- Topology modification: Prune, root, collapse nodes, resolve polytomies
- Distance calculations: Compute branch lengths and topological distances between nodes
- Tree comparison: Calculate Robinson-Foulds distances and identify topological differences
Common patterns:
from ete3 import Tree
## Basic statistics
print(f"Leaves: {len(tree)}")
print(f"Total nodes: {len(list(tree.traverse()))}")
## Prune to taxa of interest
taxa_to_keep = ["species1", "species2", "species3"]
tree.prune(taxa_to_keep, preserve_branch_length=True)
Use cases
- Use etetoolkit to prepare publication-quality figures.
- Apply etetoolkit when results need clear visual communication.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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