Research Topics
| Alexei J DrummondSummaryAffiliation: University of Auckland Country: New Zealand Publications
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Detail Information
Publications
Bayesian phylogenetics with BEAUti and the BEAST 1.7Alexei J Drummond
Department of Computer Science, University of Auckland, Auckland, New Zealand
Mol Biol Evol 29:1969-73. 2012..BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk...- Fully Bayesian tests of neutrality using genealogical summary statisticsAlexei J Drummond
Bioinformatics Institute, University of Auckland, Auckland, New Zealand
BMC Genet 9:68. 2008..Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome... - Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1Charles T T Edwards
Nuffield Department of Clinical Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
BMC Evol Biol 6:28. 2006..Despite this, the magnitude of this population bottleneck is unclear... - BEAST: Bayesian evolutionary analysis by sampling treesAlexei J Drummond
Bioinformatics Institute, University of Auckland, Auckland, New Zealand
BMC Evol Biol 7:214. 2007..A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented... - Bayesian random local clocks, or one rate to rule them allAlexei J Drummond
Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
BMC Biol 8:114. 2010..Thus, including both the global molecular clock and the unconstrained model results, there are a total of 2(2n-2) possible rate models available for averaging with 1, 2, ..., 2n - 2 different rate categories... - Bayesian inference of species trees from multilocus dataJoseph Heled
Department of Computer Science, University of Auckland, New Zealand
Mol Biol Evol 27:570-80. 2010..We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation... - Calibrated tree priors for relaxed phylogenetics and divergence time estimationJoseph Heled
Department of Computer Science, University of Auckland, Auckland, New Zealand
Syst Biol 61:138-49. 2012..Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis... 
Mapping the origins and expansion of the Indo-European language familyRemco Bouckaert
Department of Computer Science, University of Auckland, Auckland 1142, New Zealand
Science 337:957-60. 2012..These results highlight the critical role that phylogeographic inference can play in resolving debates about human prehistory...- Phylogenetic and epidemic modeling of rapidly evolving infectious diseasesDenise Kühnert
Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
Infect Genet Evol 11:1825-41. 2011.... - Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogeneticsWai Lok Sibon Li
Computational Evolution Group, University of Auckland, Auckland, New Zealand
Mol Biol Evol 29:751-61. 2012..Our methods are implemented under the BEAST 1.6 software package, available at http://beast-mcmc.googlecode.com... - Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte CarloChieh Hsi Wu
University of Auckland, Auckland 1001, New Zealand
Genetics 188:151-64. 2011..Simulated data are used to evaluate our method in terms of accuracy and precision of estimation and also identification of the true mutation model. Finally we apply our method to a red colobus monkey data set as an example... - Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence dataAlexei J Drummond
School of Biological Sciences, University of Auckland 1001, Auckland, New Zealand
Genetics 161:1307-20. 2002..We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences... - Bayesian inference of population size history from multiple lociJoseph Heled
Department of Computer Science, University of Auckland, Auckland, New Zealand
BMC Evol Biol 8:289. 2008..Here we present the Extended Bayesian Skyline Plot, a non-parametric Bayesian Markov chain Monte Carlo algorithm that extends a previous coalescent-based method in several ways, including the ability to analyze multiple loci... - Bayesian selection of nucleotide substitution models and their site assignmentsChieh Hsi Wu
Department of Computer Science, University of Auckland, Auckland, New Zealand
Mol Biol Evol 30:669-88. 2013..In some instances, this improved modeling of the substitution process can have a measurable effect on downstream inference, including the estimated phylogeny, relative divergence times, and effective population size histories... - How accurate and robust are the phylogenetic estimates of Austronesian language relationships?Simon J Greenhill
Department of Psychology, University of Auckland, Auckland, New Zealand
PLoS ONE 5:e9573. 2010..The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations...