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|Whelan S, Allen JE, Blackburne BP, et al. (2015) ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models. Systematic Biology. 64: 42-55|
|Allen JE, Whelan S. (2014) Assessing the state of substitution models describing noncoding RNA evolution. Genome Biology and Evolution. 6: 65-75|
|Kersey PJ, Allen JE, Christensen M, et al. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research. 42: D546-52|
|Cooper JD, Smyth DJ, Smiles AM, et al. (2008) Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nature Genetics. 40: 1399-401|