Root Digger: a root placement program for phylogenetic trees. - Ben Bettisworth; Alexandros Stamatakis (BMC Bioinform., 2021)

A LASSO-based approach to sample sites for phylogenetic tree search. - Noa Ecker; Dana Azouri; Ben Bettisworth; Alexandros Stamatakis; Yishay Mansour; Itay Mayrose; Tal Pupko (Bioinform., 2022)

Uncommon Problems in Phylogenetic Inference - Ben Bettisworth (2023)

Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods. - Ben Bettisworth; Alexander I. Jordan; Alexandros Stamatakis (Stat. Comput., 2023)