Andrew Rambaut

The proximal origin of SARS-CoV-2

SARS-CoV-2 is the seventh coronavirus known to infect humans; SARSCoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mi...

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary...

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequenc...

SARS-CoV-2 variants, spike mutations and immune escape

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and an...

BEAST: Bayesian evolutionary analysis by sampling trees

BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statis...

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of mol...

Bayesian Phylogeography Finds Its Roots

As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately...

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest i...

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

Research aimed at understanding the geographic context of evolutionary histories is burgeoning across biological disciplines. Recent endeavors attempt to interpret contemporaneo...

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

Abstract Summary: SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial–temporal diffusio...

Many-core algorithms for statistical phylogenetics

Abstract Motivation: Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allo...

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutati...

Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories

DNA sequences extracted from ancient remains are increasingly used to generate large population data sets, often spanning tens of thousands of years of population history. Bayes...

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular B...

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-b...

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development...

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

Seq-Gen can be obtained by WWW from http:/(/)evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html++ + or by FTP from ftp:/(/)evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the ...