1. AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees
- Author
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Bastien Cazaux, Eric Rivals, Guillaume Castel, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and French National Research Agency (ANR) : ANR-11-BINF-0002
- Subjects
Interactive visualisation ,Statistics and Probability ,Computer science ,MESH: Biological Evolution G05.045.513 ,[SDV]Life Sciences [q-bio] ,analyse phylogénétique ,computer.software_genre ,Biochemistry ,03 medical and health sciences ,Inference ,Phylogenetics ,Biologie animale ,Molecular Biology ,Phylogeny ,030304 developmental biology ,Animal biology ,0303 health sciences ,Phylogenetic tree ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,030302 biochemistry & molecular biology ,Uncertainty ,Probabilistic logic ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Web ,Computer Science Applications ,Visualization ,Phylogeography ,Computational Mathematics ,Tree (data structure) ,Phenotype ,Computational Theory and Mathematics ,arbre phylogénétique ,Data mining ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,computer ,Tree ,Software - Abstract
Motivation 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. Results 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). Availability and implementation AQUAPONY is coded in JavaScript/HTML, available under Cecill license, and can be freely used at http://www.atgc-montpellier.fr/aquapony/.
- Published
- 2019