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

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)

MorphBank, The Development of a General Purpose Bioinformatics Database. - Fredrik Ronquist; Gregory A. Riccardi; David Gaitros; Neelima Jammigumpula; Wifredo Blanco (International Conference on Internet Computing, 2005)

A Biodiversity Semantic Associative Annotation Tool. - David Gaitros; Wei Zhang; Austin Mast; Gregory A. Riccardi; Fredrik Ronquist (International Conference on Internet Computing, 2006)

Automatic Alignment of Sequential Monte Carlo Inference in Higher-Order Probabilistic Programs. - Daniel Lundén; David Broman; Fredrik Ronquist; Lawrence M. Murray (CoRR, 2018)

Probabilistic Programming for Birth-Death Models of Evolution Using an Alive Particle Filter with Delayed Sampling. - Jan Kudlicka; Lawrence M. Murray; Fredrik Ronquist; Thomas B. Schön (UAI, 2019)

Universal Probabilistic Programming Language Compilation with Parallel Efficient Sequential Monte Carlo Inference. - Daniel Lundén; Joey Öhman; Jan Kudlicka; Viktor Senderov; Fredrik Ronquist; David Broman (CoRR, 2021)

Compiling Universal Probabilistic Programming Languages with Efficient Parallel Sequential Monte Carlo Inference. - Daniel Lundén; Joey Öhman; Jan Kudlicka; Viktor Senderov; Fredrik Ronquist; David Broman (ESOP, 2022)

Automatic Alignment in Higher-Order Probabilistic Programming Languages. - Daniel Lundén; Gizem Çaylak; Fredrik Ronquist; David Broman (ESOP, 2023)

ASV portal: an interface to DNA-based biodiversity data in the Living Atlas. - Maria Prager; Daniel Lundin; Fredrik Ronquist; Anders F. Andersson (BMC Bioinform., 2023)