SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

被引：423

作者：

Bielejec, Filip ^{[1
]}

Rambaut, Andrew ^{[2
,3
]}

Suchard, Marc A. ^{[4
,5
,6
]}

Lemey, Philippe ^{[1
]}

机构：

[1] Katholieke Univ Leuven, Rega Inst Med Res, Clin & Epidemiol Virol Sect, Louvain, Belgium

[2] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland

[3] NIH, Fogarty Int Ctr, Bethesda, MD 20892 USA

[4] Univ Calif Los Angeles, Dept Biomath, Los Angeles, CA USA

[5] Univ Calif Los Angeles, Dept Biostat, Los Angeles, CA USA

[6] Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 20期

基金：

欧洲研究理事会; 美国国家卫生研究院;

关键词：

PHYLOGEOGRAPHY;

D O I：

10.1093/bioinformatics/btr481

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2910 / 2912

页数：3

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