Patel, V R , et al., Circadioomics: Integrating Circadian Genomics, Transcriptomics, Proteomics and Metabolomics. Nature Methods, 2012. 9(8): 772-773.
The statistical selection of best-fit models of nucleotide substitution is routine in the phylogenetic analysis of DNA sequence alignments. With the advent of next-generation sequencing technologies, most researchers are moving from phylogenetics to phylogenomics, in which large sequence alignments typically include hundreds or thousands of loci. Phylogenetic resources therefore need to be adapted to a high-performance computing paradigm so as to allow demanding analyses at the genomic level. Here we introduce jModelTest 2, a program for nucleotide-substitution model selection that incorporates more models, new heuristics, efficient technical optimizations and parallel computing.