Visualization of continuous phylogeographic reconstructions

EvoLaps aims at visualizing spatio-temporal spread of epidemics, from Maximum Clade Credibility (MCC) tree obtained by continuous phylogeographic inference. Changes of localities (transitions), in a "Top-Down" reading of the tree (from the root to its leaves), are represented on a cartographic background using paths between them. The bundle of paths is a phylogeographic scenario.

A raw reading of these transitions produces complex scenarios, and EvoLaps helps to analyze them with brush selection, animation, highlight processes, but also with the possibility of discretizing the continuous localities into clusters of regions using different methods/tools of clustering (lasso, anchor, clade selection, dynamic latitude/longitude grid, K-means). The dynamic EvoLaps clustering is iterative, allowing more or less detailed phylogeographic scenarios according to specific spatio-temporal phases of it. For instance, an analysis starts with a small number of large clusters, and selected clusters can be subdivided afterwards for having a higher resolution.

EvoLaps also offers tools to corroborate third party variables to the phylogeographic scenario such as the superimposition of heat maps, or the computation of ancestral character states from discrete variables.


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

Citation Chevenet F, Fargette D, Guindon S, Bañuls AL. EvoLaps: a web interface to visualize continuous phylogeographic reconstructions. BMC Bioinformatics. 2021 Sep 27;22(1):463. doi: 10.1186/s12859-021-04386-z. PMID: 34579644; PMCID: PMC8474961.
Chevenet et al., 2021


Funding This work has been supported by The 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, and support from the Agence Nationale pour la Recherche through the grant GENOSPACE.

Thanks D. Hubert for system administration and A. Prudhon for English editing

API Icons by Icon8 ⦙ D3 ⦙ Leaflet ⦙ Leaflet-Heat ⦙ jquery ⦙ jscolor ⦙ svg-export ⦙ kmeans ⦙ bezierjs-master

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