This site is for the research, software and publications of Andrew Rambaut and members of his research group.

News

The BEAST software package has its own website: http://beast.bio.ed.ac.uk

We now have a site for posting analyses and news about emerging infectious diseases: http://epidemic.bio.ed.ac.uk/. This includes a new section on the novel human 2c genotype coronavirus.

 
A special issue of Phil. Trans. Roy. Soc. B on “Next Generation Molecular & Evolutionary Epidemiology of Infectious Disease” is now available: http://rstb.royalsocietypublishing.org/content/368/

 
Recent publications
Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic.
Diehl WE, Lin AE, Grubaugh ND, et al. (2016) Cell 167, 1088-1098.
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.
Dudas G, Carvalho LM, Trevor Bedford, et al. (2016) bioRxiv 071779
The Evolution of Ebola virus: Insights from the 2013-2016 Epidemic.
Holmes EC, Dudas G, Rambaut A, et al. (2016) Nature 538, 193-200.
MERS-CoV recombination: implications about the reservoir and potential for adaptation.
Dudas G & Rambaut A (2016) Virus Evolution 2, vev023.
Real-time, portable genome sequencing for Ebola surveillance.
Quick J, Loman NJ, Duraffour S, et al. (2016) Nature 530, 228-232.
Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set .
Hall M, Woolhouse M & Rambaut A (2015) PLOS Comput Biol 11, e1004613.
Evolution and Spread of Ebola Virus in Liberia, 2014-2015.
Ladner JT, Wiley MR, Mate S, et al. (2015) Cell Host and Microbe 18, 659-669.
Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone.
Park DJ, Dudas G, Wohl S, et al. (2015) Cell 161, 1516-1526.
Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.
Carroll MW, Matthews DA, Hiscox JA, et al. (2015) Nature 524, 97-101.
Global circulation patterns of seasonal influenza viruses vary with antigenic drift.
Bedford T, Riley S, Barr I, et al. (2015) Nature 523, 217-220.

Latest software
2016-10-04 - FigTree
Produce high-quality figures of phylogenetic trees
2016-06-17 - BEAST
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
2016-04-01 - TempEst
Explore temporal signal and clocklikeness in trees (formerly Path-O-Gen)
2013-12-11 - Tracer
A program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes
2011-10-28 - Seq-Gen
An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phyloge(...)
2008-11-29 - TreeStat
A program that calculates summary statistics of a set of trees
2002-12-01 - Phylogen
2002-10-04 - TreeEdit

 
Andrew Rambaut, 2007