tree-formatting

Format phylogenetic trees with ggtree or iTOL layouts and overlays.

2|Updated Feb 18, 2026

Search Tags:#taxonomy #phylogenetics #ggtree #itol #tree-visualization #clades

Ready to run

npx skills add https://github.com/MusserLab/lab-claude-skills --skill tree-formatting

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: tree-formatting
Source: https://github.com/MusserLab/lab-claude-skills/tree/main/skills/tree-formatting
Command: npx skills add https://github.com/MusserLab/lab-claude-skills --skill tree-formatting

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Phylogenetic tree visualization and formatting with ggtree (R) or iTOL (web). Use when rendering a phylogenetic tree as a figure, choosing tree layout, coloring branches or labels by taxonomy, collapsing clades, displaying support values, or adding overlays to a tree. Do NOT load for tree inference (use protein-phylogeny skill) or domain annotation (future separate skill).

Core Features & Use Cases

Choose rendering backend (ggtree or iTOL) based on offline vs interactive needs.
Stepwise workflow to select tree type, collapsing strategy, labeling level, and rooting.
Templates and guidance for ggtree (collapsed rectangular, collapsed circular) and iTOL (annotation and upload workflows), with gotchas and best practices.

Quick Start

Render a phylogenetic tree with the chosen backend (ggtree or iTOL) and apply taxonomy-based coloring, collapsing, and overlays as guided.

Frequently Asked Questions about tree-formatting

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

FAQPage Schema

How do I format a phylogenetic tree for a publication-ready figure?▼

Format phylogenetic trees by selecting a rendering backend like ggtree or iTOL, then customize layout, apply taxonomy-based coloring, collapse clades, and add overlays to generate publication-ready figures.

What's the best way to color phylogenetic tree branches by taxonomy?▼

Color phylogenetic tree branches by taxonomy using ggtree or iTOL templates. The skill guides you through backend-specific annotation workflows to apply taxonomy-based coloring reliably.

Does this skill support tree inference and phylogenetic reconstruction?▼

No, this skill explicitly does not support tree inference or phylogenetic reconstruction. It focuses strictly on visualizing and formatting existing phylogenetic trees; use a protein-phylogeny skill for inference tasks.

Can I use iTOL for offline phylogenetic tree visualization?▼

No, iTOL is a web-based interactive tool. For offline phylogenetic tree visualization and formatting, choose the ggtree backend in R to generate publication-ready figures locally.

How do I collapse clades in a circular phylogenetic tree?▼

Collapse clades in a circular phylogenetic tree by applying the provided collapsed circular templates in ggtree or adjusting clade collapsing strategies within the iTOL annotation workflow.

What are the limitations of using ggtree for tree visualization?▼

ggtree is limited to formatting and visualizing existing phylogenetic trees in R, not inferring them. Users must navigate specific gotchas and apply provided templates to avoid unreliable visual outputs.