Real-time analysis of Ebola virus evolution
Legend
Frequencies
Input mutations as position+nucleotide, i.e. 8926C to plot its frequency through time.
Feature explanation

Use the date slider to adjust sampling window.

Use the drop down menu to color viruses geographic region, sampling date, or local branching index.

Click on variable sites to specify positions to color viruses by genotype.

Mouse over a tip to show virus name, location and features.

click on a branch to zoom into its descendent clade.

The local branching index is the exponentially weighted tree length surrounding a node, which is associated with rapid branching and expansion of clades. A more detailed explanation is available here. Retrospective analysis has shown that LBI correlates with clade growth.

Acknowledgements

We thank:

European Mobile Lab (EMLab) Carroll et al. (2015)
the Viral Hemorrhagic Fever Consortium: Kenema Government Hospital, Broad Institute, Harvard University, Tulane University, University of Edinburgh (VHFC1 and VHFC2) Gire et al. (2014) and Park et al. (2015)
China CDC and the State Key Laboratory of Pharmaceutical Biotechnology (SKLPB) Tong et al. (2015)
the Centers for Disease Control and Prevention (CDC) Park et al. (2015)
the United States Army Medical Research Institute of Infectious Diseases (USAMRIID) Kugelman et al. (2015)
University of Cambridge/Wellcome Trust Sanger/Public Health England (UoC/WT/PHE) Goodfellow et al. (2015)
European Mobile Lab/University of Cambridge/Wellcome Trust Sanger (EMLab/UoC/WT) Goodfellow et al. (2015)
European Mobile Lab and the University of Birmingham (EMLab-RT) Loman et al. (2015)
Public Health England (PHE) Bell et al. (2015)
Institut Pasteur (IP) Simon-Loriere et al. (2015)
Dutch Mobile Lab (DML) Smits, Koopmans et al. (2015)
National Institute of Allergy and Infectious Diseases (NIAID) Hoenen et al. (2015)
National Institute for Infectious Diseases IRCCS, Italy (INMI) Capobianchi et al. (2015)
Genetic Medicine and Development, University of Geneva, Switzerland (CHE_UoG) Kaiser et al. (2015)
for generously sharing EBOV sequence data. We also thank Andrew Rambaut for leadership and coordination of data sharing and analysis efforts.


Built by Trevor Bedford and Richard Neher. Give us a shout at @trvrb or @richardneher with questions or comments. All source code is freely available under the terms of the GNU Affero General Public License. Data updated and processed with commit .

© 2015 Trevor Bedford and Richard Neher