Visualising very large phylogenetic trees in three dimensional hyperbolic space. - Timothy Hughes; Young Hyun; David A. Liberles (BMC Bioinform., 2004)

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data. - Roald Rossnes; Ingvar Eidhammer; David A. Liberles (BMC Bioinform., 2005)

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. - Christian Roth 006; Matthew J. Betts; Pär Steffansson; Gisle Sælensminde; David A. Liberles (Nucleic Acids Res., 2005)

On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention. - Ashley I. Teufel; Jing Zhao; Malgorzata M. O'Reilly; Liang Liu; David A. Liberles (Comput., 2014)

Evolutionary Models. - David A. Liberles; Barbara R. Holland (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events. - C. Nicholas Henry; Kathryn Piper; Amanda E. Wilson; John L. Miraszek; Claire S. Probst; Yuying Rong; David A. Liberles (BMC Bioinform., 2022)

PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways. - Nicholas S. McCloskey; Ayna Mammedova; David A. Liberles (BMC Bioinform., 2024)