bio-phylo-tree-visualization
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing colors and labels, exporting to image formats, or choosing between Bio.Phylo, ggtree, ETE4, and iTOL for publication.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tree-visualization --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, matplotlib 3.8+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Tree Visualization **"Create a publication-quality tree figure"** → Draw and customize phylogenetic tree visualizations with colored branches, tip labels, and bootstrap support values using matplotlib. - Python: `Bio.Phylo.draw()` with matplotlib customization Draw phylogenetic trees using matplotlib integration. Bio.Phylo provides basic rectangular tree plots suitable for quick visualization. For publication-quality figures with complex annotations, circular layouts, or metadata heatmaps, consider the alternatives below. ## Visualization Tool Decision | Tool | Type | Best For | Limitations | |------|------|----------|-------------| | Bio.Phylo + matplotlib | Python | Quick rectangular plots, scripted pipelines | No circular/radial layouts, limited annotation | | **ggtree** (R/
- Version Compatibility
- Visualization Tool Decision
- Required Import
- ASCII Tree Display
- Basic Tree Drawing
- Customizing Tree Appearance
- Label Customization
- Branch Labels (Bootstrap, Lengths)
- Coloring Trees
- Highlighting Clades
- Multiple Output Formats
- Figure Size and Layout
- Phylo.draw() Parameters
- Pre-Processing for Better Visualization
What does the bio-phylo-tree-visualization skill do?
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing colors and labels, exporting to image formats, or choosing between Bio.Phylo, ggtree, ETE4, and iTOL for publication.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tree-visualization --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.