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PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context.

Pieter Libin1,2, Ewout Vanden Eynden1, Francesca Incardona3

  • 1Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium.

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Summary

PhyloGeoTool offers a visual method for exploring large virus phylogenetic trees and their geographic spread. This tool aids in understanding pathogen evolution and informing public health interventions.

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Area of Science:

  • Genomics
  • Epidemiology
  • Bioinformatics

Background:

  • Understanding pathogen epidemic spread in space and time is crucial for optimizing public health interventions.
  • Large virus sequence databases offer opportunities to study pathogen dissemination through phylogenetic analysis.
  • Efficient exploration of large phylogenetic trees is needed to extract meaningful insights.

Purpose of the Study:

  • To develop an efficient and visual method for exploring large phylogenetic trees.
  • To annotate clades with strain characteristics and geographic context.
  • To enable interactive data exploration for public health research.

Main Methods:

  • PhyloGeoTool implements a visual and interactive approach for phylogenetic tree exploration.
  • The tool depicts strain and clade characteristics, including geographic context.
  • It allows positioning new virus strains within existing phylogenies without re-analysis.

Main Results:

  • PhyloGeoTool provides an interactive visual method for exploring large phylogenetic trees.
  • Strain characteristics and geographic context can be effectively depicted.
  • New virus strains can be placed within existing trees for rapid insight.

Conclusions:

  • PhyloGeoTool facilitates the exploration of large phylogenetic datasets for epidemiological studies.
  • The software aids in understanding pathogen spread and informing public health strategies.
  • It offers a valuable tool for researchers studying virus evolution and dissemination.