etetoolkit

Name: etetoolkit
Availability: InStock
Author: jaechang-hits

Analyze and visualize phylogenetic trees using the ETE Toolkit Python library.

298|27|Updated Feb 18, 2026

Search Tags:#bioinformatics #visualization #evolutionary biology #phylogenetics #tree analysis #ncbi taxonomy

Ready to run

npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill etetoolkit-jaechang-hits

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/etetoolkit
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill etetoolkit-jaechang-hits

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ete3, numpy, lxml, PyQt5, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the complex process of analyzing, manipulating, and visualizing phylogenetic trees, making evolutionary insights accessible.

Core Features & Use Cases

Tree Parsing & I/O: Load and save trees in various formats (Newick, PhyloXML, NHX).
Annotation & Traversal: Add metadata to nodes and navigate complex tree structures.
Visualization: Generate publication-quality tree figures with customizable styles.
Taxonomy Integration: Map species to NCBI taxonomy for lineage analysis.
Use Case: You have a Newick file representing gene family evolution. Use this Skill to annotate nodes with duplication events, visualize the tree with branch lengths proportional to evolutionary distance, and export it as a high-resolution PNG.

Quick Start

Use the etetoolkit skill to load the tree from 'my_tree.nwk' and print the names of all leaf nodes.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema

How do I visualize a phylogenetic tree from a Newick file in Python?▼

To visualize phylogenetic trees from Newick files, you can parse the file and render publication-quality figures with customizable styles. This Skill uses the ETE3 library to load Newick formats and export high-resolution images like PNG.

Can I add node annotations to a phylogenetic tree and traverse its structure?▼

Yes, you can add metadata annotations to nodes and navigate complex tree structures. The Skill supports tree traversal and node annotation, allowing you to mark events like duplications directly within Newick, NHX, or PhyloXML formats.

How does NCBI taxonomy integration work for phylogenetic tree analysis?▼

NCBI taxonomy integration maps species within your phylogenetic tree to their taxonomic lineages. This allows you to perform evolutionary biology and comparative genomics analysis by linking tree leaves to the NCBI taxonomy database.

What phylogenetic tree formats are supported for parsing and visualization?▼

Supported phylogenetic tree formats include Newick, NHX, and PhyloXML. The Skill parses these formats to facilitate tree manipulation, node annotation, and the generation of publication-quality visualizations for evolutionary biology research.

Do I need PyQt5 to render publication-quality phylogenetic tree figures?▼

Yes, PyQt5 is a required dependency for rendering publication-quality phylogenetic tree figures. Alongside numpy and lxml, PyQt5 provides the graphical framework needed by the ETE3 toolkit to generate high-resolution visual outputs.

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

Analyzing gene family evolution involves loading a Newick tree, annotating nodes with duplication events, and visualizing branch lengths proportional to evolutionary distance. This Skill provides the ETE3 functionality needed to execute this comparative genomics workflow.