PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

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

Abstract: 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.