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Phylogenetic Trees03:21

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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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A Practical Guide to Phylogenetics for Nonexperts
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PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.

Lukasz Kreft1, Alexander Botzki1, Frederik Coppens2,3

  • 1VIB Bioinformatics Core, VIB, 9052 Ghent, Belgium.

Bioinformatics (Oxford, England)
|May 20, 2017
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Summary

A new open-source tool, PhyD3, offers advanced visualization for phylogenetic trees using current web technologies. This tool supports functional genomics and annotation datasets, enhancing comparative and evolutionary studies.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic trees are crucial for analyzing and visualizing biological data in comparative and evolutionary studies.
  • Existing web-based tools for phylogenetic tree visualization have limitations, with a lack of feature-rich, open-source solutions using modern web technologies.

Purpose of the Study:

  • To develop a state-of-the-art, open-source web-based tool for advanced phylogenetic tree visualization.
  • To extend the PhyloXML standard for enhanced annotation capabilities.

Main Methods:

  • Developed PhyD3, a lightweight tool utilizing the JavaScript library D3.js.
  • Extended the PhyloXML standard to incorporate functional genomics and annotation datasets.
  • Implemented an open-source solution for easy adaptation and integration into third-party websites.

Main Results:

  • PhyD3 provides state-of-the-art phylogenetic tree visualization directly in web browsers.
  • The tool supports advanced annotations and is compatible with functional genomics data.
  • The PhyloXML standard was extended to better accommodate complex biological datasets.

Conclusions:

  • PhyD3 offers a versatile and accessible open-source solution for advanced phylogenetic tree visualization.
  • The enhanced PhyloXML standard and PhyD3 tool facilitate more sophisticated analysis and display of evolutionary data.
  • This development addresses the need for a feature-rich, modern, open-source tool in bioinformatics.