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

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. - Arlin Stoltzfus; Hilmar Lapp; Naim Matasci; Helena F. Deus; Brian Sidlauskas; Christian M. Zmasek; Gaurav Vaidya; Enrico Pontelli; Karen Cranston; Rutger A. Vos; Campbell O. Webb; Luke J. Harmon; et al. (BMC Bioinform., 2013)

Neutral Models of Microbiome Evolution. - Qinglong Zeng; Jeet Sukumaran; Steven H. Wu; Allen G. Rodrigo (PLoS Comput. Biol., 2015)

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

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes. - Thomas K. F. Wong; Teng Li; Louis Ranjard; Steven H. Wu; Jeet Sukumaran; Allen G. Rodrigo (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)

Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space. - Jeet Sukumaran; Marina Meila (BMC Bioinform., 2024)