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README.md

Phylogeography of Zika virus from 1997 - Sep 2017

This analysis was produced using data collected and generated as part of a large collaborative study to identify how Zika virus spread to Florida, USA during the 2016-16 Zika virus pandemic. For more details, please see Grubaugh et al. 2017. The video shows the spatio-temporal diffusion of viral lineages between 1997 and 2017 that was generated by reconstructing the ancestral phylogeny of Zika virus.

All genomic sequences used in the analysis are publicly available on GenBank. Tree was generated using BEAST v1.8.4 under a SRD06 nucleotide substitution model and a relaxed molecular clock along with a Bayesian Skyline model. The BEAST XML file is available in data. The phylogeographic diffusion process was realised using a discrete state asymmetric CTMC.

Rendered video is for use under CC-BY-SA-4 and available in movie.

Rendered video on Youtube.

Inspired by Phylogeography of 2014-2015 Ebola virus epidemic by Gytis Dudas.

Dependencies

Made with Natural Earth.

Natural Earth

License

All content outside of data/ is licensed under CC-BY-SA-4. Natural Earth shapefiles in data/ne_10m_admin_0_countries/ are in public domain.


Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
data@andersen-lab.com