期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 33, 期 8, 页码 2167-2169出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msw082
关键词
SpreaD3; SPREAD; BEAST; phylogenetics; phylogeography; Bayesian inference; visualization; Java; JavaScript; D3; Google Earth; KML; software; JSON; GeoJSON
资金
- European Union [278433-PREDEMICS]
- ERC [260864]
- European Union's Horizon 2020 Research and Innovation Programme [634650-VIROGENESIS, 643476-COMPARE]
- National Institutes of Health [R01 AI107034, R01 HG006139, LM011827]
- National Science Foundation [IIS 1251151, DMS 1264153]
- Research Fund KU Leuven
- Research Grant of the Research Foundation - Flanders (FWO
- Fonds Wetenschappelijk Onderzoek - Vlaanderen)
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.
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