DendroPy: a Python library for phylogenetic computing. - Jeet Sukumaran; Mark T. Holder (Bioinform., 2010)

Phylesystem: a git-based data store for community-curated phylogenetic estimates. - Emily Jane McTavish; Cody E. Hinchliff; James F. Allman; Joseph W. Brown; Karen Cranston; Mark T. Holder; Jonathan Rees; Stephen A. Smith (Bioinform., 2015)

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

DendroPy 5: a mature Python library for phylogenetic computing. - Matthew Andres Moreno; Mark T. Holder; Jeet Sukumaran (J. Open Source Softw., 2024)