EvoLaps is a user-friendly web application designed to visualize the spatial and temporal spread of pathogens. It takes an annotated tree as input, such as a maximum clade credibility tree obtained through phylogeographic inference. By following a top-down reading of the tree, transitions (latitude/longitude changes from a node to its children) are represented on a cartographic background using graphical paths. The complete set of paths forms the phylogeographic scenario. A raw reading of these transitions can produce complex scenarios. EvoLaps helps analyze them with:
  • 2D/3D visualization of scenarios with multiple layouts and extensive style customization,
  • multiple graphical variables with time-dependent gradients for enhanced path display,
  • cross-highlighting and selection between the phylogenetic tree and the phylogeographic scenario,
  • clustering of localities into spatial clusters to generate synthetic views,
  • animation of the phylogeographic scenario using phylogenetic tree brushing,
  • support for both discrete and continuous model analyses,
  • a customizable geographic map with support for environmental data layers,
  • interactive phylogenetic tree editing,

Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa. (Bangura et al., 2024)

EvoLaps video showcase
Contact
  • francois.chevenet@ird.fr if you would like to use EvoLaps and see it evolve with the integration of new features (modeling in epidemiology, phylogenetics, phylodynamics), feel free to contact me.
Funding
  • ANRS-24-PEPR MIE-0003 PEPR MIE 2024. PReViX project (Pandemic preparedness to Respiratory Virus X)
  • Agence Nationale pour la Recherche through the grant GENOSPACE ANR-16-CE02-0008.
  • PALADIN project, publicly funded through the French National Research Agency under the “Investissements d’avenir” program with the reference ANR-10-LABX-04-01 Labex CEMEB.
Warning
  • 'Shift' load EvoLaps to refresh the cache of the navigator. Hold down the 'Shift' key while clicking the reload button, or 'command' key (or CTRL key) + R
API Citation
  • EvoLaps version 3 - Chevenet F, Vitré T, Cadar D, Fichet-Calvet E, Fargette D, Bastide P, Guindon S. EvoLaps 3: Next-Level phylogeographic visualization. under construction
  • EvoLaps version 2 - Chevenet F, Fargette D, Bastide P, Vitré T, Guindon S. EvoLaps 2: Advanced phylogeographic visualization. Virus Evol. 1 janv 2024;10(1):vead078.
  • EvoLaps version 1 - Chevenet F, Fargette D, Guindon S, Bañuls AL. EvoLaps: a web interface to visualize continuous phylogeographic recon- structions. BMC Bioinformatics. 27 sept 2021;22(1):463.
Thanks
  • D. Hubert for system administration
  • A. Prudhon for English editing
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