title: SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.
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.
authors.affiliation: Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium filip.bielejec@rega.kuleuven.be.
authors.forename: Filip
authors.initials: F
authors.lastname: Bielejec
authors.affiliation: Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium.
authors.forename: Guy
authors.initials: G
authors.lastname: Baele
authors.affiliation: Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium.
authors.forename: Bram
authors.initials: B
authors.lastname: Vrancken
authors.affiliation: 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.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D019143:Evolution, Molecular; D020407:Internet; D010641:Phenotype; D010802:Phylogeny; D012984:Software
keywords: BEAST; Bayesian inference; D3; GeoJSON.; Google Earth; JSON; Java; JavaScript; KML; SPREAD; SpreaD3; phylogenetics; phylogeography; software; visualization