MRBAYES: Bayesian inference of phylogenetic trees. - John P. Huelsenbeck; Fredrik Ronquist (Bioinform., 2001)

Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-Values. - Rasmus Nielsen; John P. Huelsenbeck (Pacific Symposium on Biocomputing, 2002)

MrBayes 3: Bayesian phylogenetic inference under mixed models. - Fredrik Ronquist; John P. Huelsenbeck (Bioinform., 2003)

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. - Gautam Altekar; Sandhya Dwarkadas; John P. Huelsenbeck; Fredrik Ronquist (Bioinform., 2004)