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Genome Biology and Evolution|January 7, 2014
Assessing the state of substitution models describing noncoding RNA evolutionJames E Allen, Simon WhelanSystematic Biology|September 12, 2014
ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution modelsSimon Whelan, James E Allen, Benjamin P Blackburne, et al.Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences|October 15, 2008
The genetic code can cause systematic bias in simple phylogenetic modelsSimon WhelanSystematic Biology|September 13, 2007
New approaches to phylogenetic tree search and their application to large numbers of protein alignmentsSimon WhelanMolecular Biology and Evolution|May 27, 2008
Spatial and temporal heterogeneity in nucleotide sequence evolutionSimon WhelanMolecular Biology and Evolution|November 2, 2002
A novel use of equilibrium frequencies in models of sequence evolutionNick Goldman, Simon WhelanGenetics|September 3, 2004
Estimating the frequency of events that cause multiple-nucleotide changesSimon Whelan, Nick GoldmanSystematic Biology|November 15, 2011
Characterizing the phylogenetic tree-search problemDaniel Money, Simon WhelanBioinformatics (Oxford, England)|March 1, 2015
GeLL: a generalized likelihood library for phylogenetic modelsDaniel Money, Simon WhelanPageof 6