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Rodrigue, N. and Lartillot, N. (2014). Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package. Bioinformatics, 30:1020-1021. Dettman, J. R., Rodrigue, N., Aaron, S. D. and Kassen, R. (2013). Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A., 110:21065-21070. Rodrigue, N. (2013). On the statistical interpretation of site-specific variables in phylogeny-based substitution models. Genetics, 193:557-564. Dettman, J. R., Rodrigue, N., Melnyk, A. H., Wong, A., Bailey, S. F., and Kassen, R. (2012). Evolutionary insights from whole-genome sequencing of experimentally evolved microbes. Mol. Ecol. 20:2058-2077. Rodrigue, N., Philippe, H. and Lartillot, N. (2010). Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc. Natl. Acad. Sci. U. S. A., 107:4629-4634.