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Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

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Updated: Aug 27, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

tidy tree: A New Layout for Phylogenetic Trees.

Simon Penel¹, Damien M de Vienne¹

¹Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.

Molecular Biology and Evolution

|September 26, 2022

Summary

A new non-layered tidy tree layout improves phylogenetic tree visualization by reducing empty space. This method enhances readability for large evolutionary trees in limited print or screen areas.

Keywords:

phylogram tree layout visualization

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Last Updated: Aug 27, 2025

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Published on: February 5, 2014

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Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Phylogenetic tree visualization is crucial for understanding evolutionary relationships.
Large phylogenies pose challenges for readability due to limited space and high zoom levels.
Existing tree layouts often result in significant empty space, reducing efficiency.

Purpose of the Study:

To implement and evaluate the non-layered tidy tree layout for phylogenetic visualization.
To demonstrate the advantages of this layout in reducing drawing space and improving readability.
To encourage the integration of this novel layout into phylogenetic software.

Main Methods:

Implementation of the non-layered tidy tree layout algorithm in R language.
Application of the layout to both simulated and real biological data, including the measles virus phylogeny.
Integration of the layout as a function in the R package 'ape' and the tool 'thirdkind'.

Main Results:

The non-layered tidy tree layout effectively reduces empty space in phylogenetic tree visualizations.
This layout enhances the readability of large and complex evolutionary trees.
Demonstrated advantages on simulated data and a real measles virus phylogeny.

Conclusions:

The non-layered tidy tree layout offers a significant improvement for visualizing large phylogenetic trees.
Its implementation in R and other tools facilitates wider adoption.
This layout should be integrated into standard phylogenetic software for better data representation.