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AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees.

Authors
  • Cazaux, Bastien1, 2
  • Castel, Guillaume2, 3
  • Rivals, Eric1, 2
  • 1 Department of Computer Science, LIRMM, UMR 5506, CNRS and Université Montpellier, Montpellier, France. , (France)
  • 2 Institut de Biologie Computationelle, Montpellier, France. , (France)
  • 3 Forest, Grassland and Freshwater Ecology, CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France. , (France)
Type
Published Article
Journal
Bioinformatics (Oxford, England)
Publication Date
Sep 01, 2019
Volume
35
Issue
17
Pages
3163–3165
Identifiers
DOI: 10.1093/bioinformatics/btz011
PMID: 30649190
Source
Medline
Language
English
License
Unknown

Abstract

The visualization and interpretation of evolutionary spatiotemporal scenarios is broadly and increasingly used in infectious disease research, ecology or agronomy. Using probabilistic frameworks, well-known tools can infer from molecular data ancestral traits for internal nodes in a phylogeny, and numerous phylogenetic rendering tools can display such evolutionary trees. However, visualizing such ancestral information and its uncertainty on the tree remains tedious. For instance, ancestral nodes can be associated to several geographical annotations with close probabilities and thus, several migration or transmission scenarios exist. We expose a web-based tool, named AQUAPONY, that facilitates such operations. Given an evolutionary tree with ancestral (e.g. geographical) annotations, the user can easily control the display of ancestral information on the entire tree or a subtree, and can view alternative phylogeographic scenarios along a branch according to a chosen uncertainty threshold. AQUAPONY interactively visualizes the tree and eases the objective interpretation of evolutionary scenarios. AQUAPONY's implementation makes it highly responsive to user interaction, and instantaneously updates the tree visualizations even for large trees (which can be exported as image files). AQUAPONY is coded in JavaScript/HTML, available under Cecill license, and can be freely used at http://www.atgc-montpellier.fr/aquapony/. © The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected]

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