STEM: species tree estimation using maximum likelihood for gene trees under coalescence. - Laura Salter Kubatko; Bryan C. Carstens; L. Lacey Knowles (Bioinform., 2009)

Occupancy spectrum distribution: application for coalescence simulation with generic mergers. - Arnaud Becheler; L. Lacey Knowles (Bioinform., 2020)

Incorporating the speciation process into species delimitation. - Jeet Sukumaran; Mark T. Holder; L. Lacey Knowles (PLoS Comput. Biol., 2021)