Manipulate phylogenetic trees with Newick, NHX, PhyloXML, and NeXML formats.
npx skills add https://github.com/jackspace/ClaudeSkillz --skill etetoolkit
Please help me install this Agent Skill. Skill: etetoolkit Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-pkg-etetoolkit Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill etetoolkit
ETE Toolkit provides a robust suite for manipulating, analyzing, and visualizing phylogenetic trees, with NCBI taxonomy integration and advanced tree operations.
Load a tree, prune taxa, root at midpoint, and render a PDF visualization.
High-intent search queries and answers about installing and using this skill.
Phylogenetic trees can be loaded from Newick, NHX, PhyloXML, and NeXML formats, then manipulated through traversal, pruning, rooting, and node collapsing operations. ETE Toolkit supports all these formats and operations natively, enabling rapid tree preprocessing for analysis.
Yes, NCBI Taxonomy integration allows you to annotate and lookup taxonomic information directly within tree nodes. This enables taxonomy-aware analysis and validation of evolutionary relationships alongside your tree structure.
ETE Toolkit computes pairwise distances between nodes, RF distance metrics, and detects evolutionary events like orthologs and paralogs through gene-tree reconciliation. These analyses reveal evolutionary relationships and divergence patterns.
Publication-quality tree visualizations render to PNG, PDF, and SVG formats. This allows seamless integration into documents and publications with customizable layout and styling.
Yes, orthology and paralogy inference is supported through gene-tree reconciliation methods. These analyses identify orthologs and paralogs to understand functional relationships across species.
Tree analysis reveals evolutionary topology, divergence times, and functional relationships beyond sequence similarity. Use trees when you need orthology detection, evolutionary event dating, or comparative genomics across multiple species.
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