PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. - Whelan, Simon; Irisarri, Iker; Burki, Fabien (Bioinform., 2018)

GeLL: a generalized likelihood library for phylogenetic models. - Money, Daniel; Whelan, Simon (Bioinform., 2015)

Determining the evolutionary history of gene families. - Ames, Ryan M.; Money, Daniel; Ghatge, Vikramsinh P.; Whelan, Simon; Lovell, Simon C. (Bioinform., 2012)

Measuring the distance between multiple sequence alignments. - Blackburne, Benjamin P.; Whelan, Simon (Bioinform., 2012)

Determination and validation of principal gene products. - Tress, Michael L.; Wesselink, Jan-Jaap; Frankish, Adam; López, Gonzalo; Goldman, Nick; Löytynoja, Ari; Massingham, Tim; Pardi, Fabio; Whelan, Simon; Harrow, Jennifer L.; Valencia, Alfonso (Bioinform., 2008)

Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome. - Kosiol, Carolin; Bofkin, Lee; Whelan, Simon (J. Biomed. Informatics, 2006)

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. - Whelan, Simon; Bakker, Paul I. W. de; Quevillon, Emmanuel; Rodriguez, Nicolas; Goldman, Nick (Nucleic Acids Res., 2006)

Pandit: a database of protein and associated nucleotide domains with inferred trees. - Whelan, Simon; Bakker, Paul I. W. de; Goldman, Nick (Bioinform., 2003)