PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

Pieter Libin, Ewout Vanden Eynden, Francesca Incardona, Ann Nowé, Antonia Bezenchek, Anders Sönnerborg, Anne-Mieke Vandamme, Kristof Theys, Guy Baele, EucoHIV study group

Research output: Contribution to journalArticlepeer-review


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 interactiveway. 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: (Freely available: open source software project).

Supplementary information: Supplementary information is available at Bioinformatics online.

Original languageEnglish
Publication statusE-pub ahead of print - 26 Aug 2017


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