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etetoolkit

Manipulate, analyze, and visualize phylogenetic trees in Newick, NHX, and PhyloXML formats.

Updated Jan 10, 2026
Search Tags:#bioinformatics#evolutionary biology#phylogenetics#ete toolkit#tree analysis#ncbi taxonomy
One-click install
npx skills add https://github.com/robinbarvaag/poynt --skill etetoolkit-robinbarvaag
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/robinbarvaag/poynt/tree/main/.github/skills/etetoolkit
Command: npx skills add https://github.com/robinbarvaag/poynt --skill etetoolkit-robinbarvaag

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies complex phylogenetic tree analysis, manipulation, and visualization, making advanced bioinformatics accessible.

Core Features & Use Cases

  • Tree Manipulation: Load, modify, prune, and root trees in various formats (Newick, NHX).
  • Phylogenetic Analysis: Detect evolutionary events (duplication, speciation), identify orthologs.
  • Taxonomy Integration: Connect trees with NCBI Taxonomy for annotation.
  • Visualization: Generate publication-quality tree figures (PDF, SVG, PNG).
  • Use Case: Analyze gene family evolution by detecting duplications, identifying orthologs, and visualizing the resulting species trees.

Quick Start

Use the etetoolkit skill to visualize the tree in 'my_tree.nw' as a PDF file.

Frequently Asked Questions about etetoolkit

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I visualize and render a phylogenetic tree as a publication-quality image?▼

To visualize a phylogenetic tree, you can load tree files in Newick, NHX, or PhyloXML formats and render them directly into publication-quality PDF, SVG, or PNG images for downstream use.

How do I detect evolutionary events like gene duplication and speciation in a phylogenetic tree?▼

Detecting evolutionary events such as duplication and speciation involves analyzing the phylogenetic tree structure to automatically identify orthologs and infer gene family evolution patterns.

Can I integrate NCBI taxonomy data to annotate my phylogenetic tree?▼

Yes, you can integrate NCBI taxonomy by connecting your phylogenetic tree with the NCBI Taxonomy database, enabling accurate taxonomic annotation and species tree validation.

What phylogenetic tree formats are supported for loading and manipulating trees?▼

Supported phylogenetic tree formats include Newick, NHX, and PhyloXML, allowing you to load, modify, prune, and root trees seamlessly across various phylogenomic workflows.

What is the best way to analyze gene family evolution using phylogenomic workflows?▼

Analyzing gene family evolution is best achieved by integrating sequence alignments with your phylogenetic tree to detect duplications, identify orthologs, and visualize resulting species trees.

Does this toolkit require external dependencies for tree I/O and manipulation?▼

No external dependencies are required for tree I/O and manipulation, as the standalone toolkit inherently supports loading, modifying, pruning, and rooting trees natively.

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