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
- Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.
- Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A & Robertson DL (2012) BMC Bioinformatics 13, 47.
- APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete "All or Nothing" Phenomenon. .
- Armitage AE, Deforche K, Chang C-H, Wee E, Kramer B, Welch JJ, Gerstoft J, Fugger L, McMichael A, Rambaut A & Iversen AKN (2012) PLoS Genetics 8, e1002550.
- Bayesian phylogenetics with BEAUti and the BEAST 1.7.
- Drummond AJ, Suchard MA, Dong Xie & Rambaut A (2012) Mol Biol Evol 29, 1969-1973.
- BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics.
- Ayres D, Darling A, Zwickl D, Beerli P, Holder M, Lewis P, Huelsenbeck JP, Ronquist F, Swofford D, Cummings MP, Rambaut A & Suchard MA (2012) Syst Biol 61, 170-173.
- Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.
- Raghwani J, Rambaut A, Holmes EC, Vu Ty Hang, Tran Tinh Hien, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR & Simmons CP (2011) PLoS Pathog 7, e1002064.
- A Bayesian phylogenetic method to estimate unknown sequence ages.
- Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG & Rambaut A (2010) Mol Biol Evol 28, 879-887.
- Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses.
- Firth C, Kitchen A, Shapiro A, Suchard MA, Holmes EC & Rambaut A (2010) Mol Biol Evol 27, 2038-2051.
- Phylogeography takes a relaxed random walk in continuous space and time.
- Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol 27, 1877-1886.
- Bayesian Phylogeography Finds Its Roots.
- Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Comput Biol 5, e1000520.
- Evolutionary analysis of the dynamics of viral infectious disease.
- Pybus OG & Rambaut A (2009) Nature Reviews Genetics 10, 540-550.
Latest software
- 2013-04-23 - Path-O-Gen
- Explore temporal signal and clocklikeness in trees
- 2012-12-05 - FigTree
- Produce high-quality figures of phylogenetic trees
- 2011-10-28 - Seq-Gen
- An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phyloge(...)
- 2009-11-30 - Tracer
- A program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes
- 2008-11-29 - TreeStat
- A program that calculates summary statistics of a set of trees
- 2002-12-01 - Phylogen
- 2002-10-04 - TreeEdit
