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)

Molecular Clock. - Cara Van Der Wal; Simon Y. W. Ho (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)