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

doi:10.1093/bioinformatics/btx535

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 journal › Article › peer-review

Abstract

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.

Original language	English
Journal	Bioinformatics
DOIs	https://doi.org/10.1093/bioinformatics/btx535
Publication status	E-pub ahead of print - 26 Aug 2017

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10.1093/bioinformatics/btx535

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@article{159d28a2e25e44d2936ca4ece84be767,

title = "PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context",

abstract = "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.",

author = "Pieter Libin and {Vanden Eynden}, Ewout and Francesca Incardona and Ann Now{\'e} and Antonia Bezenchek and Anders S{\"o}nnerborg and Anne-Mieke Vandamme and Kristof Theys and Guy Baele and {EucoHIV study group}",

year = "2017",

month = aug,

day = "26",

doi = "10.1093/bioinformatics/btx535",

language = "English",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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TY - JOUR

T1 - PhyloGeoTool

T2 - interactively exploring large phylogenies in an epidemiological context

AU - Libin, Pieter

AU - Vanden Eynden, Ewout

AU - Incardona, Francesca

AU - Nowé, Ann

AU - Bezenchek, Antonia

AU - Sönnerborg, Anders

AU - Vandamme, Anne-Mieke

AU - Theys, Kristof

AU - Baele, Guy

AU - EucoHIV study group

PY - 2017/8/26

Y1 - 2017/8/26

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btx535

DO - 10.1093/bioinformatics/btx535

M3 - Article

C2 - 28961923

SN - 1367-4803

JO - Bioinformatics

JF - Bioinformatics

ER -

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

Abstract

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