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Updated: Dec 26, 2025

A Practical Guide to Phylogenetics for Nonexperts
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Using ggtree to Visualize Data on Tree-Like Structures.

Guangchuang Yu1

  • 1Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.

Current Protocols in Bioinformatics
|March 13, 2020
PubMed
Summary
This summary is machine-generated.

The ggtree package suite, including treeio, tidytree, and ggtree, offers versatile tools for visualizing diverse tree-like data beyond phylogenetics. It enables comprehensive data presentation and analysis across multiple scientific disciplines.

Keywords:
grammar of graphicsphylogenytree associated datatree structurevisualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Visualization

Background:

  • The ggtree package suite has evolved over five years to support tree-like data visualization.
  • It integrates tree data input/output (treeio) and manipulation (tidytree) with visualization (ggtree).
  • Originally for phylogenetic trees, its scope now includes other tree structures.

Purpose of the Study:

  • To present five basic protocols for visualizing tree-like structures and associated data using the ggtree package.
  • To demonstrate the application of ggtree in various biological and data science disciplines.
  • To showcase the flexibility of ggtree in handling diverse tree data and analyses.

Main Methods:

  • Utilizing the grammar of graphics syntax for tree visualization.
  • Visualizing hierarchical clustering results and associated data.
  • Estimating and visualizing bootstrap values on trees.
  • Estimating and visualizing continuous and discrete ancestral traits.
  • Visualizing multiple sequence alignments alongside phylogenetic trees.

Main Results:

  • Demonstrated five distinct protocols for tree data visualization using ggtree.
  • Showcased the package's ability to integrate tree data manipulation and visualization.
  • Extended the application of ggtree to diverse tree-like structures beyond phylogenetics.
  • Provided practical examples for analyzing and presenting complex biological data.

Conclusions:

  • The ggtree package suite provides a powerful and flexible platform for visualizing various tree-like structures and associated data.
  • Its modular design (treeio, tidytree, ggtree) facilitates efficient data handling and presentation.
  • ggtree extends the visualization capabilities to a broader range of scientific disciplines, enhancing data interpretation.