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bio-phylo-tree-visualization

Draw and export phylogenetic tree figures with Bio.Phylo, matplotlib, ggtree, ETE4, or iTOL.

Updated Sep 15, 2026
Search Tags:#bioinformatics#matplotlib#biopython#phylogenetics#newick#ggtree#tree visualization
One-click install
npx skills add https://github.com/mrsonord2240/openscience-specialists --skill bio-phylo-tree-visualization-mrsonord2240
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-phylo-tree-visualization
Source: https://github.com/mrsonord2240/openscience-specialists/tree/main/specialists/molecular-phylogenetics-analyst/versions/1.0.0/package/skills/bio-phylo-tree-visualization
Command: npx skills add https://github.com/mrsonord2240/openscience-specialists --skill bio-phylo-tree-visualization-mrsonord2240

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, matplotlib.

What problem does it solve? Phylogenetic tree figures silently encode interpretive choices—layout geometry, ladderization, root placement, and unlabeled support values—that can mislead readers, and common tools like Bio.Phylo silently drop BEAST HPD annotations or cannot render circular layouts. ## Core Features & Use Cases - Tool and layout selection: Routes between Bio.Phylo (quick Python plots), ggtree + treeio (publication figures with metadata and BEAST HPD bars), ETE4 (programmatic styling), and iTOL (large trees), with tip-count thresholds guiding rectangular vs circular layouts. - Honest support display: Parses IQ-TREE SH-aLRT/UFBoot dual labels, names the support measure in legends, and applies measure-specific thresholds (bootstrap >=95, SH-aLRT >=80, UFBoot >=95, posterior >=0.95). - Publication export: Saves vector SVG/PDF figures with scale bars, branch coloring by clade, and caption declarations of layout, length units, and ladderization disclaimers. - Use Case: A researcher with a 600-tip IQ-TREE result gets a circular ggtree figure with dual SH-aLRT/UFBoot support labeled by measure, while a BEAST chronogram is routed through treeio so its 95% HPD node-age bars are preserved. ## Quick Start Ask the agent to read your Newick tree file, draw it as a phylogram with support values labeled by their measure, and export it as a vector PDF.

Frequently Asked Questions about bio-phylo-tree-visualization

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

FAQPage Schema
How do I draw a phylogenetic tree in Python with Bio.Phylo?▼

Read the tree with Phylo.read, optionally ladderize it, then call Phylo.draw with a matplotlib axes and do_show=False, followed by fig.savefig to a PDF or SVG. Bio.Phylo renders rectangular layouts only.

ggtree vs Bio.Phylo for phylogenetic tree figures?▼

Bio.Phylo suits quick scripted rectangular plots inside Python pipelines, while ggtree with treeio is the publication standard for circular layouts, metadata heatmaps, dual support labels, and BEAST HPD bars. Bio.Phylo cannot parse BEAST annotation blocks.

Why are my BEAST HPD bars missing from the tree figure?▼

Bio.Phylo flattens trees to topology plus one label and silently drops BEAST HPD intervals and posteriors. Route the tree through treeio read.beast and plot with ggtree geom_range using center = 'height' to place bars correctly.

How do I show SH-aLRT and UFBoot support values on an IQ-TREE tree?▼

IQ-TREE dual labels like '88/97' stay in clade.name with confidence set to None, so split the string on the slash and assign the values to custom attributes. Label both measures in the legend since they use different scales and thresholds.

What layout should I use for a tree with hundreds of tips?▼

Rectangular layouts with horizontal labels stay legible up to roughly 150 tips; beyond that switch to circular or fan layouts with radial labels. Past about 500-1000 tips, annotate with colored strips or rings in ggtreeExtra or iTOL instead of per-tip text.

Should I export phylogenetic trees as PNG or PDF for publication?▼

Export vector formats such as SVG, PDF, or EPS so thin branches and small tip labels stay sharp at any print size. Only rasterize if a journal forces it, at final size with at least 600 dpi for line art.

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