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

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

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

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

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

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

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

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