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Phylogenetic Trees03:21

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Taxonium, a web-based tool for exploring large phylogenetic trees.

Theo Sanderson1

  • 1The Francis Crick Institute, London, United Kingdom.

Elife
|November 15, 2022
PubMed
Summary

The COVID-19 pandemic generated massive SARS-CoV-2 sequencing data. A new tool, Taxonium, enables visualization of large viral phylogenetic trees in browsers, aiding variant and transmission analysis.

Keywords:
epidemiologyevolutionary biologygenomicsglobal healthphylogeneticsphylogenytreevirusvirusesweb

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Area of Science:

  • Genomics
  • Computational Biology
  • Virology

Background:

  • The COVID-19 pandemic has led to an unprecedented volume of SARS-CoV-2 genome sequencing.
  • Phylogenetic trees are crucial for understanding viral evolution, transmission, and variant emergence.
  • Existing tools struggle to visualize the massive SARS-CoV-2 phylogenetic datasets.

Purpose of the Study:

  • To develop a scalable web-based tool for exploring large phylogenetic trees.
  • To enable the visualization and analysis of mutation-annotated trees with millions of nodes.
  • To provide insights into SARS-CoV-2 evolution using large-scale phylogenetic analysis.

Main Methods:

  • Development of Taxonium, a novel tool utilizing WebGL for browser-based phylogenetic tree exploration.
  • Integration of metadata linking and support for mutation-annotated trees.
  • Deployment options including local browser execution, server-based backend, and desktop application.

Main Results:

  • Taxonium successfully visualizes phylogenetic trees with tens of millions of nodes directly in the browser.
  • Analysis of a five-million-sequence SARS-CoV-2 tree provided insights into viral evolution.
  • A public tree of over five million SARS-CoV-2 sequences is available for exploration at cov2tree.org.

Conclusions:

  • Taxonium overcomes the scalability limitations of previous tools for large phylogenetic datasets.
  • The tool facilitates the identification of transmission events and the emergence of SARS-CoV-2 variants.
  • Taxonium is a versatile tool applicable to any phylogenetic tree and is available for broader use.