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Publication

PhyloGeoTool

Journal Contribution - Journal Article

Subtitle:interactively exploring large phylogenies in an epidemiological context

Motivation: Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.

Results: PhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.

Availability and implementation: https://github.com/rega-cev/phylogeotool (Freely available: open source software project).

Contact: phylogeotool@kuleuven.be.

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal: Bioinformatics
ISSN: 1367-4803
Issue: 24
Volume: 33
Pages: 3993-3995
Publication year:2017
Keywords:Journal Article, Virus Diseases/epidemiology, Epidemiologic Methods, Humans, Software, Phylogeny, Computational Biology/methods, Databases, Nucleic Acid, Cluster Analysis
BOF-keylabel:yes
CSS-citation score:1
Authors:International
Authors from:Higher Education
Accessibility:Open