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/
Recent publications
- 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.
- Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.
- Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JSM, Guan Y & Rambaut A (2009) Nature 459, 1122-1125.
- Pandemic Potential of a Strain of Influenza A (H1N1) : Early Findings.
- Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Apluche-Aranda CM, Chapela IB, Zavala EP, Guevara DME, Checchi E, Garcia E, Hugonnet S, Roth C & and The WHO Rapid Pandemic Assessment Collaboration. 2009. (2009) Science 324, 1557-1561.
- Many-Core Algorithms for Statistical Phylogenetics.
- Suchard MA & Rambaut A (2009) Bioinformatics 25, 1370-1376.
- Accommodating the effect of ancient DNA damage on inferences of demographic histories.
- Rambaut A, Ho SYW, Drummond AJ & Shapiro B (2008) Mol Biol Evol 26, 245-248.
- The Genomic and Epidemiological Dynamics of Human Influenza A Virus.
- Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK & Holmes EC (2008) Nature 453, 615-619.
- Correlates of substitution rate variation in mammalian protein-coding sequences.
- Welch JJ, Bininda-Emonds ORP & Bromham L (2008) BMC Evol Biol 8, 53.
- Estimation of 2Nes from temporal allele frequency data.
- Bollback JP, York T & Nielsen R (2008) Genetics In press
- BEAST: Bayesian Evolutionary Analysis Sampling Trees.
- Drummond AJ & Rambaut A (2007) BMC Evolutionary Biology 7, 214.
Latest software
- 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
- 2009-11-27 - Path-O-Gen
- Explore temporal signal and clocklikeness in trees
- 2009-03-04 - MK-Test
- Maximum likelihood multi-locus McDonald-Kreitman Tests
- 2008-11-29 - TreeStat
- A program that calculates summary statistics of a set of trees
- 2008-07-07 - MLE.time-average.trait.R
- R script for ML estimation of time-averaged trait values
- 2005-01-07 - Seq-Gen
- An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phyloge(...)
- 2002-12-01 - Phylogen
- 2002-10-04 - TreeEdit