Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package von Rodrigue, Nicolas, Lartillot, Nicolas

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Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles von Rodrigue, Nicolas, Philippe, Hervé, Lartillot, Nicolas

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Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa von Dettman, Jeremy R., Rodrigue, Nicolas, Aaron, Shawn D., Kassen, Rees

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Heterotachy and long-branch attraction in phylogenetics von Philippe, Hervé, Zhou, Yan, Brinkmann, Henner, Rodrigue, Nicolas, Delsuc, Frédéric

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Detecting amino acid preference shifts with codon-level mutation-selection mixture models von Kazmi, S Omar, Rodrigue, Nicolas

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PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment von Lartillot, Nicolas, Rodrigue, Nicolas, Stubbs, Daniel, Richer, Jacques

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On the statistical interpretation of site-specific variables in phylogeny-based substitution models von Rodrigue, Nicolas

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A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes von Rodrigue, Nicolas, Latrille, Thibault, Lartillot, Nicolas

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Genomics of Compensatory Adaptation in Experimental Populations of Aspergillus nidulans von Dettman, Jeremy R, Rodrigue, Nicolas, Schoustra, Sijmen E, Kassen, Rees

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A Bayesian mutation-selection framework for detecting site-specific adaptive evolution in protein-coding genes (vol 38, pg 1199, 2021) von Rodrigue, Nicolas, Latrille, Thibault, Lartillot, Nicolas

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The effect of selection environment on the probability of parallel evolution von Bailey, Susan F, Rodrigue, Nicolas, Kassen, Rees

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A maximum likelihood framework for protein design von Kleinman, Claudia L, Rodrigue, Nicolas, Bonnard, Cécile, Philippe, Hervé, Lartillot, Nicolas

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COMPASS: the COMPletely Arbitrary Sequence Simulator von Low, Andrew, Rodrigue, Nicolas, Wong, Alex

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models von Laurin-Lemay, Simon, Rodrigue, Nicolas, Lartillot, Nicolas, Philippe, Hervé

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Clonal evolution and genome stability in a 2500-year-old fungal individual von Anderson, James B., Bruhn, Johann N., Kasimer, Dahlia, Wang, Hao, Rodrigue, Nicolas, Smith, Myron L.

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Grouping substitution types into different relaxed molecular clocks von Lee, Hui-Jie, Kishino, Hirohisa, Rodrigue, Nicolas, Thorne, Jeffrey L.

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Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa von Dettman, Jeremy R, Rodrigue, Nicolas, Kassen, Rees

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Statistical potentials for improved structurally constrained evolutionary models von Kleinman, Claudia L, Rodrigue, Nicolas, Lartillot, Nicolas, Philippe, Hervé

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Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models von Rodrigue, Nicolas, Philippe, Hervé, Lartillot, Nicolas

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Fast Bayesian Choice of Phylogenetic Models: Prospecting Data Augmentation-Based Thermodynamic Integration von Rodrigue, Nicolas, Aris-Brosou, Stéphane

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