PAL: an object-oriented programming library for molecular evolution and phylogenetics. - Alexei J. Drummond; Korbinian Strimmer (Bioinform., 2001)

Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. - Gerton Lunter; István Miklós; Alexei J. Drummond; Jens Ledet Jensen; Jotun Hein (WABI, 2003)

A Brief Introduction to the Phylogentics Analysis Library V1.5. - Matthew Goode; Korbinian Strimmer; Alexei J. Drummond; Ed Buckler; Allen G. Rodrigo (APBC, 2004)

Bayesian coestimation of phylogeny and sequence alignment. - Gerton Lunter; István Miklós; Alexei J. Drummond; Jens Ledet Jensen; Jotun Hein (BMC Bioinform., 2005)

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)

Clock-constrained tree proposal operators in Bayesian phylogenetic inference. - Sebastian Höhna; Michael Defoin-Platel; Alexei J. Drummond (BIBE, 2008)

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

A retrodictive stochastic simulation algorithm. - Timothy G. Vaughan; Peter D. Drummond; Alexei J. Drummond (J. Comput. Phys., 2010)

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. - Matthew Kearse; Richard Moir; Amy Wilson; Steven Stones-Havas; Matthew Cheung; Shane S. Sturrock; Simon Buxton; Alex Cooper; Sidney Markowitz; Chris Duran; Tobias Thierer; Bruce Ashton; et al. (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)

Recursive algorithms for phylogenetic tree counting. - Alexandra Gavryushkina; David Welch 003; Alexei J. Drummond (Algorithms Mol. Biol., 2013)

Efficient Bayesian inference under the structured coalescent. - Timothy G. Vaughan; Denise Kühnert; Alex Popinga; David Welch 003; Alexei J. Drummond (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)

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. - Alexandra Gavryushkina; David Welch 003; Tanja Stadler; 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)

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)

Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. - Jing Yang; Nicola F. Müller; Remco R. Bouckaert; Bing Xu 001; Alexei J. Drummond (PLoS Comput. Biol., 2019)

Bayesian inference and comparison of stochastic transcription elongation models. - Jordan Douglas; Richard Kingston; Alexei J. Drummond (PLoS Comput. Biol., 2020)

Bayesian inference of the climbing grade scale. - Alexei J. Drummond; Alex Popinga (CoRR, 2021)

LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses. - Alexei J. Drummond; Kylie Chen; Fábio K. Mendes; Dong Xie (PLoS Comput. Biol., 2023)

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities. - Lars Berling; Jonathan Klawitter; Remco R. Bouckaert; Dong Xie; Alex Gavryushkin; Alexei J. Drummond (PLoS Comput. Biol., 2025)

Credible Sets of Phylogenetic Tree Topology Distributions. - Jonathan Klawitter; Alexei J. Drummond (CoRR, 2025)