ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. - Sebastián Duchêne; Martyna Molak; Simon Y. W. Ho (Bioinform., 2014)

Mammalian genome evolution is governed by multiple pacemakers. - Sebastián Duchêne; Simon Y. W. Ho (Bioinform., 2015)

Estimating the number and assignment of clock models in analyses of multigene datasets. - Sebastián Duchêne; Charles S. P. Foster; Simon Y. W. Ho (Bioinform., 2016)

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. - Sebastián Duchêne; Jemma L. Geoghegan; Edward C. Holmes; Simon Y. W. Ho (Bioinform., 2016)

PhyloMAd: efficient assessment of phylogenomic model adequacy. - David A. Duchêne; Sebastián Duchêne; Simon Y. W. Ho (Bioinform., 2018)

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)

Phytest: quality control for phylogenetic analyses. - Wytamma Wirth; Simon J. Mutch; Robert Turnbull; Sebastián Duchêne (Bioinform., 2022)

Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal. - John H. Tay; Arthur Kocher; Sebastián Duchêne (PLoS Comput. Biol., 2024)

How does date-rounding affect phylodynamic inference for public health? - Leo A. Featherstone; Danielle J. Ingle; Wytamma Wirth; Sebastián Duchêne (PLoS Comput. Biol., 2025)