Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. - Andy Purvis; Andrew Rambaut (Comput. Appl. Biosci., 1995)

Bi-De: an application for simulating phylogenetic processes. - Andrew Rambaut; Nicholas C. Grassly; Sean Nee; Paul H. Harvey (Comput. Appl. Biosci., 1996)

PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. - Nicholas C. Grassly; Jun Adachi; Andrew Rambaut (Comput. Appl. Biosci., 1997)

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. - Andrew Rambaut; Nicholas C. Grassly (Comput. Appl. Biosci., 1997)

End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences. - Andrew Rambaut; Paul H. Harvey; Sean Nee (Comput. Appl. Biosci., 1997)

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. - Andrew Rambaut (Bioinform., 2000)

GENIE: estimating demographic history from molecular phylogenies. - Oliver G. Pybus; Andrew Rambaut (Bioinform., 2002)

Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. - Koen Deforche; Ricardo Camacho; Kristel Van Laethem; Beth Shapiro; Yves Moreau; Andrew Rambaut; Anne-Mieke Vandamme; Philippe Lemey (J. Comput. Biol., 2007)

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. - Philippe Lemey; Sergei L. Kosakovsky Pond; Alexei J. Drummond; Oliver G. Pybus; Beth Shapiro; Helena Barroso; Nuno Taveira; Andrew Rambaut (PLoS Comput. Biol., 2007)

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. - Koen Deforche; Ricardo Camacho; Kristel Van Laethem; Philippe Lemey; Andrew Rambaut; Yves Moreau; Anne-Mieke Vandamme (Bioinform., 2008)

Many-core algorithms for statistical phylogenetics. - Marc A. Suchard; Andrew Rambaut (Bioinform., 2009)

The RNA Virus Database. - Robert Belshaw; Tulio de Oliveira; Sidney Markowitz; Andrew Rambaut (Nucleic Acids Res., 2009)

Bayesian Phylogeography Finds Its Roots. - Philippe Lemey; Andrew Rambaut; Alexei J. Drummond; Marc A. Suchard (PLoS Comput. Biol., 2009)

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach. - John P. Archer; Andrew Rambaut; Bruce E. Taillon; P. Richard Harrigan; Marilyn Lewis; David L. Robertson (PLoS Comput. Biol., 2010)

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. - Filip Bielejec; Andrew Rambaut; Marc A. Suchard; Philippe Lemey (Bioinform., 2011)

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. - John P. Archer; Greg Baillie; Simon J. Watson 002; Paul Kellam; Andrew Rambaut; David L. Robertson (BMC Bioinform., 2012)

Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework. - Bram Vrancken; Andrew Rambaut; Guy Baele; Anne-Mieke Vandamme; Kristel Van Laethem; Eric Van Wijngaerden; Alexei J. Drummond; Marc A. Suchard; Philippe Lemey (IWBBIO, 2013)

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. - Filip Bielejec; Philippe Lemey; Luiz Carvalho; Guy Baele; Andrew Rambaut; Marc A. Suchard (BMC Bioinform., 2014)

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. - Remco R. Bouckaert; Joseph Heled; Denise Kühnert; Timothy G. Vaughan; Chieh-Hsi Wu; Dong Xie; Marc A. Suchard; Andrew Rambaut; Alexei J. Drummond (PLoS Comput. Biol., 2014)

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates. - Bram Vrancken; Andrew Rambaut; Marc A. Suchard; Alexei J. Drummond; Guy Baele; Inge Derdelinckx; Eric Van Wijngaerden; Anne-Mieke Vandamme; Kristel Van Laethem; Philippe Lemey (PLoS Comput. Biol., 2014)

Global circulation patterns of seasonal influenza viruses vary with antigenic drift. - Trevor Bedford; Steven Riley; Ian G. Barr; Shobha Broor; Mandeep Chadha; Nancy J. Cox; Rodney S. Daniels; C. Palani Gunasekaran; Aeron C. Hurt; Anne Kelso; Alexander Klimov; Nicola S. Lewis; et al. (Nat., 2015)

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. - Matthew Hall; Mark E. J. Woolhouse; Andrew Rambaut (PLoS Comput. Biol., 2015)

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. - Guy Baele; Philippe Lemey; Andrew Rambaut; Marc A. Suchard (Bioinform., 2017)

Virus genomes reveal factors that spread and sustained the Ebola epidemic. - Gytis Dudas; Luiz Max Carvalho; Trevor Bedford; Andrew J. Tatem; Guy Baele; Nuno R. Faria; Daniel J. Park; Jason T. Ladner; Armando Arias; Danny Asogun; Filip Bielejec; Sarah L. Caddy; et al. (Nat., 2017)

Establishment and cryptic transmission of Zika virus in Brazil and the Americas. - Nuno R. Faria; Joshua Quick; I. M. Claro; Julien Thézé; J. G. de Jesus; Marta Giovanetti; Moritz U. G. Kraemer; S. C. Hill; Allison Black; A. C. Da Costa; L. C. Franco; S. P. Silva; et al. (Nat., 2017)

Lorenzo-Redondo et al. reply. - Ramon Lorenzo-Redondo; Helen R. Fryer; Trevor Bedford; Eun-Young Kim; John A. C. Archer; Sergei L. Kosakovsky Pond; Yoon-Seok Chung; Sudhir Penugonda; Jeffrey G. Chipman; Courtney V. Fletcher; Timothy W. Schacker; Michael H. Malim; et al. (Nat., 2017)

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling. - Andrew J. Holbrook; Philippe Lemey; Guy Baele; Simon Dellicour; Dirk Brockmann; Andrew Rambaut; Marc A. Suchard (J. Comput. Graph. Stat., 2021)

SCORPIO: a utility for defining and classifying mutation constellations of virus genomes. - Rachel Colquhoun; Ben Jackson; Áine Niamh O'toole; Andrew Rambaut (Bioinform., 2023)