EvoLaps: a web interface to visualize continuous phylogeographic reconstructions

Explorations of phylogeographic reconstructions thanks to a dynamic clustering of continuous ancestral locations

EvoLaps is a free and user-friendly web interface aims to visualize phylogeographic patterns based on various clustering levels of continuous latitude/longitude from consensus phylogeographic reconstructions, along with transition diagrams that provide concise and easy to interpret summaries of phylogeographic inferences. Questions and comments welcome. francois.chevenet@ird.fr

Select one of the examples (left panel, "Demo" section) and click the "submit" button to start an analysis.

EvoLaps v25. West Nile virus (WNV) in North America, data from (Pybus et. al., 2012)

EvoLaps aims at visualizing phylogeographic scenarios, from phylogenetic trees associated with continuous localities (computed ancestral latitude/longitude pairs associated with internal nodes of the tree and sampled latitude/longitude pairs associated with the leaves of the tree).

Changes of localities, in a "Top-Down" reading of the tree (from the root to its leaves), are represented on a cartographic background using arcs between them. The bundle of arcs constitutes what we call a phylogeographic scenario.

A “raw” reading of these localities produces complex scenarios, more or less confusing from a graphical point of view, and difficult to interpret. EvoLaps helps to simplify these scenarios, by discretizing the continuous localities in the form of clusters of regions using different interactive methods/tools.

The dynamic cluster definition also allows the user to introduce his expertise, such as testing hypotheses, for instance about the spatio-temporal spread of an epidemic by adapting the geographical division (eg defining clusters according to a water network). The process is also iterative: an EvoLaps analysis can, for example, start with a small number of large clusters which will then possibly be subdivided, in order to detail a particular phase of the scenario.
EvoLaps Analysis
  • 1 Submission of a consensus of a phylogeographic reconstruction, including a newick string for the phylogenetic tree and the latitude/longitude coordinates for each node of the tree (sample and ancestral nodes).
  • 2 Clustering the sample and/or ancestral locations on the geographic map with the help of several methods: K-means algorithm and/or lasso selection and/or clade selection or meridian/parallel grid. Knowing a set of clusters and a color scale (1D or 2D), the tree is color-encoded, the transition diagram is computed. The thinner the clustering, the closer the transition diagram is to the phylogenetic tree, but more complex is the evolutionary scenario.
  • 3 Edition of the phylogeographic scenario (the set of paths between clusters) on the geographic map in a top-down reading of the transition diagram. The analysis can be iterated gradually from step two to refine the phylogeographic pattern. For instance, a session starts with a clustering defining a small number of (large) clusters, which is refined on the fly, with subdivisions of selected clusters into smaller ones up to a satisfying output.
  • 4 (optional) Compute (maximum likelihood) ancestral character states from a discrete variable, and superimpose the output to the geographic map, the phylogenetic tree and the transition diagram

  • News
    EvoLaps latest version (v.28, Sep. 2022) (clear the web navigator cache) clustering mode 1: define clusters with the help of anchors transition diagram: font size for Sz criteria scale on geographic map download/upload cluster sets new data set (example 4,RYMV) with indels polymorphism (use it to compute ancestral character states from primary annotations, discrete variable)
    Previous versions Version 27 May 2022 geographic base maps revision, including Jawg, Esri, OSM, CartoDB & Stamen tiles providers, debug of SVG export phylogenetic tree & transition diagram layouts revision, with horizontal or vertical zooms in/out, Sz text display on/off (transition diagram) user interface revision: resizable phylogenetic tree and transition diagram components, retractable control panel (EvoLaps icon) color picker from existing clusters and color cluster replacement mono color paths following the current color setting 'no clustering' option new user's manual Version 26 Apr. 2022 new library of geographic base maps (ArcGis & Open Street Maps) user interface, full window Version 25 Mar. 2022 transition diagram, new layout, taking into account branch lengths of the phylogenetic tree (full and compressed versions) transition diagram, brush selection and display of sub-evolutionary scenarios evolutionary scenario, following the transition diagram layout, ie generation or time evolutionary scenario, transient or persistent display modes evolutionary scenario, path highlight updated stripped down version of the user interface Version 24 Nov. 2021 maximum likelihood computation of ancestral character states from discrete variables and superimposition to phylogeographic scenarios full frame for each component, geographic map, phylogenetic tree and transition diagram background color for phylogenetic tree and transition diagram components EvoLaps user's manual V3 Version 23 Jul. 2021 phylogenetic tree, cartesian layout transition diagram, force-directed layout with arrows frame borders for each component bug fix, clusters with 1 or 2 members user's manual updated new demo video new demo data set (WNV) Version 22 May 2021 bugfix (path highlight from the transition diagram) Version 21 May 2021 geographic map, phylogenetic tree and transition diagram SVG export Version 20 May 2021 transition diagram new layout & bugfix Version 19 Nov. 2020
    First release

    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.


    Screenshots (click to zoom)
    EvoLaps v27. New geographic tiles providers, phylogenetic tree & transition diagram layouts revision, resizable phylogenetic tree and transition diagram components, retractable control panel, color from clusters ing, 'no clustering' option
    EvoLaps v25. transition diagram, new layout, taking into account branch lengths of the phylogenetic tree
    EvoLaps v24. Maximum likelihood computation of ancestral character states & superimposition to phylogeographic scenarios

    EvoLaps Plugin/API's
    EvoLaps server side is based on PHP, Tcl and Python scripts. EvoLaps client side is based on D3.js and Leaflet with several libraries/plugins: color2D.js, jscolor.js, leaflet-lasso, kmeans.js, bezier.js, leaflet.curve.js, leaflet-ant-path.js, svg-export.js, Leaflet.minichart,

    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.

    We thank D. Hubert for system administration and A. Prudhon for English editing