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tree-visualization

Generate publication-quality phylogenetic tree visualizations with Python matplotlib and R ggtree.

Updated Nov 20, 2025
Search Tags:#visualization#matplotlib#R#publication#phylogenetic trees#ggtree
One-click install
npx skills add https://github.com/roeimed0/rrna-phylo --skill tree-visualization
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tree-visualization
Source: https://github.com/roeimed0/rrna-phylo/tree/main/.claude/skills/tree-visualization
Command: npx skills add https://github.com/roeimed0/rrna-phylo --skill tree-visualization

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill helps researchers create publication-quality phylogenetic tree visualizations in Python and R, enabling clear communication of results and publications.

Core Features & Use Cases

  • Python Matplotlib layouts (rectangular, circular, radial) with bootstrap annotations and clade coloring.
  • R ggTree integration for publication-grade aesthetics and annotation capabilities, including export to PDF/SVG.
  • Use cases: generating figures for manuscripts, presentations, and digital repositories; interactive visualizations in notebooks.

Quick Start

Install and run templates to generate basic visualizations from your tree data. For example, start with a simple Newick tree and produce rectangular and circular layouts, then export to PDF or SVG.

Frequently Asked Questions about tree-visualization

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

FAQPage Schema
How do I create publication-quality phylogenetic tree visualizations from Newick data?▼

To create publication-quality phylogenetic tree visualizations from Newick data, use Python with matplotlib for layouts or R with ggtree for aesthetics, then export the generated figures to PDF, SVG, or PNG formats.

Can I generate circular and rectangular phylogenetic tree layouts in matplotlib?▼

Yes, you can generate circular and rectangular phylogenetic tree layouts in matplotlib. This workflow supports bootstrap annotations and clade coloring to help you prepare clear figures for manuscripts and presentations.

Does ggtree support exporting phylogenetic trees to PDF and SVG for manuscripts?▼

Yes, ggtree supports exporting phylogenetic trees to PDF and SVG for manuscripts. Using R with ggtree provides publication-grade aesthetics and annotation capabilities suitable for supplementary materials and digital repositories.

What's the best way to annotate clades and add bootstrap values to phylogenetic trees?▼

The best way to annotate clades and add bootstrap values to phylogenetic trees is using Python with matplotlib for layout control or R with ggtree for publication-grade aesthetics, enabling clear visual communication of results.

Do I need both Python and R environments to produce publication-ready phylogenetic trees?▼

You do not need both Python and R environments to produce publication-ready phylogenetic trees. You can choose Python with matplotlib for plotting or R with ggtree for visuals, depending on your preferred workflow.

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