Format phylogenetic trees with ggtree or iTOL layouts and overlays.
npx skills add https://github.com/MusserLab/lab-claude-skills --skill tree-formatting
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
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).
Render a phylogenetic tree with the chosen backend (ggtree or iTOL) and apply taxonomy-based coloring, collapsing, and overlays as guided.
High-intent search queries and answers about installing and using this skill.
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.
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.
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.
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.
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.
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.
tassiovaleAnalyze phylogenetic trees with evolutionary event detection and NCBI taxonomy integration.
bahayonghangGenerate journal-compliant academic figures from raw data using Matplotlib, Seaborn, or Plotly.
JosephWoodallQuery InterPro REST API to annotate protein function, domains, and GO terms.
MusserLabGenerate a reproducible protein phylogeny analysis script using MAFFT and IQ-TREE.
