Introduction
This site is for the research, software and publications of Andrew Rambaut and members of his research group.
Some older software packages can still be found on my old website at Oxford (now maintained by Oliver Pybus): http://evolve.zoo.ox.ac.uk.
The BEAST software package has its own website: http://beast.bio.ed.ac.uk
The Novel Human swine-origin A/H1N1 Influenza analysis site can be found here: http://influenza.bio.ed.ac.uk/
We are recruiting for a funded PhD studentship at the University of Edinburgh - starting in September 2012.
Computational approaches to understanding the molecular evolution and epidemiology of RNA viral pathogens using next generation sequencing.
We are looking for students with strong computational or statistical skills and an interest in viral infectious diseases to work on computational
problems in influenza, HIV and other diseases with serious public health implications.
This studentship is open to UK residents (or EU nationals who have been in the UK for 3 years by September). Closing date 16th March
- 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 In press
- 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.
- 2011-10-28 - Seq-Gen
- An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phyloge(...)
- 2010-11-03 - Path-O-Gen
- Explore temporal signal and clocklikeness in trees
- 2009-12-21 - FigTree
- Produce high-quality figures of phylogenetic trees
- 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
