Towards Phylogenomic Reconstruction. - Le Vinh; Andrés Varón; Daniel Janies; Ward C. Wheeler (BIOCOMP, 2007)

Maximum Parsimony on Phylogenetic networks. - Lavanya Kannan; Ward C. Wheeler (Algorithms Mol. Biol., 2012)

The tree alignment problem. - Andrés Varón; Ward C. Wheeler (BMC Bioinform., 2012)

Local search for the generalized tree alignment. - Andrés Varón; Ward C. Wheeler (BMC Bioinform., 2013)

Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. - Lavanya Kannan; Ward C. Wheeler (J. Comput. Biol., 2014)

Phylogenetic network analysis as a parsimony optimization problem. - Ward C. Wheeler (BMC Bioinform., 2015)

Efficient implied alignment. - Alex J. Washburn; Ward C. Wheeler (BMC Bioinform., 2020)