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etetoolkit

Automate manipulation, analysis, and visualization of Newick phylogenetic trees using Python's ete3 library.

Updated May 8, 2026
Search Tags:#genomics#phylogenetics#evolutionary analysis#tree visualization#tree manipulation
One-click install
npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill etetoolkit-zeyuyang-0420
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/Zeyuyang-0420/bio-ai-research-skills/tree/main/categories/bioinformatics-genomics/etetoolkit
Command: npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill etetoolkit-zeyuyang-0420

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

The etetoolkit Skill streamlines phylogenetic analysis, tree manipulation, and visualization, empowering researchers with a powerful toolkit for biological data exploration.

Core Features & Use Cases

  • Tree Manipulation: Load, manipulate, and analyze hierarchical tree structures in various formats.
  • Phylogenetic Analysis: Detect evolutionary events and analyze gene families.
  • Taxonomy Integration: Integrate NCBI taxonomy for lineage analysis.
  • Tree Visualization: Generate publication-quality visualizations.
  • Use Case: With a large gene tree and its corresponding multiple sequence alignment, you can identify duplications, speciate events, and construct a gene tree.

Quick Start

To get started with etetoolkit, first load a Newick-formatted tree file into ETE:

from ete3 import Tree
tree = Tree("gene_tree.nw")

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I automate phylogenetic tree manipulation and visualization in Python?▼

Phylogenetic tree manipulation and visualization can be automated in Python using the ete3 library. This Skill parses Newick tree files to perform complex hierarchical analysis, detect evolutionary events, and generate publication-quality tree visualizations.

What is the best way to identify gene duplications and speciation events in a phylogenetic tree?▼

Identifying gene duplications and speciation events is achieved by analyzing a gene tree alongside its multiple sequence alignment. This Skill utilizes ete3 to detect evolutionary events, analyze gene families, and annotate tree structures for evolutionary research.

Can I integrate NCBI taxonomy data for lineage analysis into my phylogenetic workflow?▼

NCBI taxonomy data can be integrated for lineage analysis within your phylogenetic workflow. This Skill leverages ete3 to combine taxonomic information with Newick tree structures, enabling detailed lineage tracking and hierarchical data exploration.

Do I need ete3 to parse Newick trees for evolutionary analysis?▼

You do need ete3 installed to parse Newick trees and perform evolutionary analysis. This Skill requires the ete3 Python library as a dependency to load, manipulate, and analyze hierarchical tree structures for genomics research.

How do I generate publication-quality visualizations from Newick formatted tree files?▼

Publication-quality visualizations from Newick formatted tree files are generated by loading the tree structure into ete3. This Skill automates the rendering process, transforming hierarchical tree data into high-quality visual outputs for biological research.

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