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lib-etetoolkit

Manipulate, analyze, and visualize phylogenetic trees with the ETE Toolkit.

Updated Mar 13, 2026
Search Tags:#bioinformatics#evolutionary biology#phylogenetics#ete toolkit#orthology#tree analysis
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-etetoolkit
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: lib-etetoolkit
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/lib-etetoolkit
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-etetoolkit

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ete3, and includes scripts (resource) and references (resource) components.

What problem does it solve?

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

Core Features & Use Cases

  • Tree Manipulation: Load, modify, and save trees in various formats (Newick, NHX).
  • Phylogenetic Analysis: Detect evolutionary events, identify orthologs, and analyze gene families.
  • Taxonomy Integration: Connect trees with NCBI taxonomy for annotation and lineage tracing.
  • Visualization: Generate publication-quality tree figures in PDF, SVG, or PNG.
  • Use Case: Analyze a large gene tree to identify orthologous genes across species and visualize the evolutionary relationships with integrated taxonomic information.

Quick Start

Use the lib-etetoolkit skill to load the tree file 'tree.nw', reroot it using the midpoint method, and save the result to 'rooted_tree.nw'.

Frequently Asked Questions about lib-etetoolkit

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

FAQPage Schema
How do I reroot a phylogenetic tree and save it in Newick format?▼

Reroot a phylogenetic tree by loading a Newick file, applying methods like midpoint rooting, and saving the modified tree to a new Newick file. This Skill provides scripts for tree manipulation, modification, and format export.

How do I identify orthologous genes across species from a phylogenetic tree?▼

Identify orthologous genes by loading a gene tree into this Skill and using its phylogenetic analysis features to detect evolutionary events and infer orthology across species within gene families.

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

Yes, you can integrate NCBI taxonomy by connecting your tree with the taxonomy database. This allows for taxonomic annotation and lineage tracing directly within your tree analysis workflow.

How do I generate publication-quality phylogenetic tree figures in PDF or SVG?▼

Generate publication-quality figures by using the visualization features to render phylogenetic trees and export them directly to PDF, SVG, or PNG formats for academic use.

Do I need Python and ete3 installed to perform phylogenetic tree analysis?▼

Yes, this Skill requires Python 3 and the ete3 package installed in your environment to execute phylogenetic tree manipulation, analysis, and visualization operations.

What is the best way to detect evolutionary events in a gene tree?▼

Detect evolutionary events by loading your gene tree into the analysis toolkit and applying the built-in functions to identify duplications, speciations, and orthology relationships.

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