SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Filip Bielejec; Guy Baele; Bram Vrancken; Marc A Suchard; Andrew Rambaut; Philippe Lemey

doi:10.1093/molbev/msw082

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Mol Biol Evol. 2016 Aug;33(8):2167-9. doi: 10.1093/molbev/msw082. Epub 2016 Apr 23.

Authors

Filip Bielejec¹, Guy Baele², Bram Vrancken², Marc A Suchard³, Andrew Rambaut⁴, Philippe Lemey²

Affiliations

¹ Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium filip.bielejec@rega.kuleuven.be.
² Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium.
³ Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles Department of Biostatistics, School of Public Health, University of California, Los Angeles.
⁴ Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom.

Abstract

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest.

Keywords: BEAST; Bayesian inference; D3; GeoJSON.; Google Earth; JSON; Java; JavaScript; KML; SPREAD; SpreaD3; phylogenetics; phylogeography; software; visualization.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bayes Theorem
Biological Evolution*
Computational Biology / methods*
Computer Graphics
Computer Simulation
Evolution, Molecular
Internet
Phenotype
Phylogeny
Software

Abstract

Publication types

MeSH terms

Grants and funding