Description
etetoolkit is an agent skill for working with phylogenetic and other hierarchical trees using ETE 4. It analyses, manipulates, compares, annotates and visualises trees. You can read Newick and Nexus tree files, inspect and annotate them, transform, root and prune them, and write them back out. It can compare topologies and calculate phylogenetic distances, find repeated subtree topologies with TreePattern, and analyse gene trees with PhyloTree. It can also query local NCBI or GTDB taxonomy databases, explore large trees interactively with SmartView, and render PNG images with SmartView or PNG, PDF and SVG output with the optional Qt tree viewer. The skill is clear about scope. ETE works with an existing tree, so it does not replace sequence alignment or phylogenetic inference software. For raw sequences you first align them, for example with MAFFT, and infer a tree with a tool such as IQ-TREE 2 or FastTree, then load the resulting tree into ETE. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…
Highlights
- Reads and writes Newick and Nexus trees
- Compares topologies and phylogenetic distances
- Queries local NCBI or GTDB taxonomy
- Interactive exploration with SmartView
- Renders PNG, PDF and SVG
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etetoolkit FAQ
What does ETE do?
It works with phylogenetic and other hierarchical trees: reading, editing, comparing, annotating and drawing them.
Can it build a tree from sequences?
No. The skill says ETE works on existing trees. Align and infer the tree with dedicated software first, then load it.
Which file formats?
Newick and Nexus tree input and output.
What can it draw?
PNG images with SmartView, and PNG, PDF or SVG with the optional Qt tree viewer.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill etetoolkit.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best etetoolkit alternatives?
Popular alternatives to etetoolkit include phylogenetics, gget and anndata. See all etetoolkit alternatives