PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. - Jeremy M. Brown; Robert ElDabaje (Bioinform., 2009)

EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics. - John J. Andersen; Bradley J. Nelson; Jeremy M. Brown (BMC Bioinform., 2016)

Investigating the Genomic Distribution of Phylogenetic Signal with CloudForest. - Reid Wagner; Benjamin S. Toups; Zhifeng Deng; Kyle A. Gallivan; Jeremy M. Brown; James C. Wilgenbusch (PEARC, 2021)