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SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

2011; Oxford University Press; Volume: 27; Issue: 20 Linguagem: Inglês

10.1093/bioinformatics/btr481

1367-4811

Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey,

Genetic diversity and population structure

Abstract Summary: SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial–temporal diffusion. The software maps phylogenies annotated with both discrete and continuous spatial information and can export high-dimensional posterior summaries to keyhole markup language (KML) for animation of the spatial diffusion through time in virtual globe software. In addition, SPREAD implements Bayes factor calculation to evaluate the support for hypotheses of historical diffusion among pairs of discrete locations based on Bayesian stochastic search variable selection estimates. SPREAD takes advantage of multicore architectures to process large joint posterior distributions of phylogenies and their spatial diffusion and produces visualizations as compelling and interpretable statistical summaries for the different spatial projections. Availability: SPREAD is licensed under the GNU Lesser GPL and its source code is freely available as a GitHub repository: https://github.com/phylogeography/SPREAD Contact: filip.bielejec@rega.kuleuven.be