Autor(es): Libin, Pieter ; Vanden Eynden, Ewout ; Incardona, Francesca ; Nowé, Ann ; Bezenchek, Antonia ; Sönnerborg, Anders ; Vandamme, Anne-Mieke ; Theys, Kristof ; Baele, Guy ; EucoHIV study group
Data: 2017
Identificador Persistente: http://hdl.handle.net/10362/180923
Origem: Repositório Institucional da UNL
Assunto(s): SDG 3 - Good Health and Well-being
Funding Information: The authors thank the EuResist Network (www.euresist.org) for providing data and the reviewers for their insightful comments which improved both the manuscript and PhyloGeoTool software. Funding Information: This work was supported by EucoHIV (www.eucohiv.org). K.T. is funded as a Postdoctoral Researcher by the Research Foundation \u2013 Flanders (FWO). P.L. is funded by a doctoral grant of the Research Foundation \u2013 Flanders (FWO) and the VUB research council [VUB/OZR2714]. G.B. acknowledges funding from the European Research Council under the European Community\u2018s Seventh Framework Programme [FP7/2007\u20132013] under Grant Agreement no. 278433-PREDEMICS. The computational resources and services used in this work were provided by the Hercules Foundation and the Flemish Government department EWI-FWO Krediet aan Navorsers [Theys, KAN2012 1.5.249.12]. The VIROGENESIS project receives funding from the European Union\u2018s Horizon 2020 Research and Innovation Programme under Grant Agreement no. 634650. Publisher Copyright: © The Author 2017. Published by Oxford University Press.
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: https://github.com/rega-cev/phylogeotool (Freely available: open source software project). Supplementary information: Supplementary information is available at Bioinformatics online.
