TY - JOUR AU - Bazykin, G. A. PY - 2015 DA - 2015// TI - Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins JO - Biol Lett VL - 11 ID - Bazykin2015 ER - TY - JOUR AU - Chen, G. -. W. AU - Chang, S. -. C. AU - Mok, C. -. K. AU - Lo, Y. -. L. AU - Kung, Y. -. N. AU - Huang, J. -. H. AU - Shih, Y. -. H. AU - Wang, J. -. Y. AU - Chiang, C. AU - Chen, C. -. J. PY - 2006 DA - 2006// TI - Genomic signatures of human versus avian influenza a viruses JO - Emerg Infect Dis VL - 12 ID - Chen2006 ER - TY - JOUR AU - Finkelstein, D. B. AU - Mukatira, S. AU - Mehta, P. K. AU - Obenauer, J. C. AU - Su, X. AU - Webster, R. G. AU - Naeve, C. W. PY - 2007 DA - 2007// TI - Persistent host markers in pandemic and h5n1 influenza viruses JO - J Virol VL - 81 ID - Finkelstein2007 ER - TY - JOUR AU - Miotto, O. AU - Heiny, A. AU - Tan, T. W. AU - August, J. T. AU - Brusic, V. PY - 2008 DA - 2008// TI - Identification of human-to-human transmissibility factors in pb2 proteins of influenza a by large-scale mutual information analysis JO - BMC Bioinformatics VL - 9 ID - Miotto2008 ER - TY - JOUR AU - Bruno, W. J. PY - 1996 DA - 1996// TI - Modeling residue usage in aligned protein sequences via maximum likelihood JO - Mol Biol Evol VL - 13 ID - Bruno1996 ER - TY - STD TI - Felsenstein J. Inferring Phylogenies. Sunderland: Sinauer associates: 2004. ID - ref6 ER - TY - BOOK AU - Yang, Z. PY - 2014 DA - 2014// TI - Molecular Evolution: a Statistical Approach PB - Oxford University Press CY - Oxford ID - Yang2014 ER - TY - JOUR AU - Blanquart, S. AU - Lartillot, N. PY - 2008 DA - 2008// TI - A site-and time-heterogeneous model of amino acid replacement JO - Mol Biol Evol VL - 25 ID - Blanquart2008 ER - TY - JOUR AU - Roure, B. AU - Philippe, H. PY - 2011 DA - 2011// TI - Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference JO - BMC Evol Biol VL - 11 ID - Roure2011 ER - TY - JOUR AU - Lartillot, N. AU - Philippe, H. PY - 2004 DA - 2004// TI - A bayesian mixture model for across-site heterogeneities in the amino-acid replacement process JO - Mol Biol Evol VL - 21 ID - Lartillot2004 ER - TY - JOUR AU - Rey, C. AU - Guéguen, L. AU - Sémon, M. AU - Boussau, B. PY - 2018 DA - 2018// TI - Accurate detection of convergent amino-acid evolution with pcoc JO - Mol Biol Evol VL - 35 ID - Rey2018 ER - TY - JOUR AU - Halpern, A. L. AU - Bruno, W. J. PY - 1998 DA - 1998// TI - Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies JO - Mol Biol Evol VL - 15 ID - Halpern1998 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 2008 DA - 2008// TI - Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage JO - Mol Biol Evol VL - 25 ID - Yang2008 ER - TY - JOUR AU - Tamuri, A. U. AU - dos Reis, M. AU - Goldstein, R. A. PY - 2012 DA - 2012// TI - Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models JO - Genetics VL - 190 ID - Tamuri2012 ER - TY - JOUR AU - Tamuri, A. U. AU - Goldman, N. AU - dos Reis, M. PY - 2014 DA - 2014// TI - A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data JO - Genetics VL - 197 ID - Tamuri2014 ER - TY - JOUR AU - Dos Reis, M. AU - Donoghue, P. C. AU - Yang, Z. PY - 2016 DA - 2016// TI - Bayesian molecular clock dating of species divergences in the genomics era JO - Nat Rev Genet VL - 17 ID - Dos Reis2016 ER - TY - JOUR AU - Rodrigue, N. PY - 2013 DA - 2013// TI - On the statistical interpretation of site-specific variables in phylogeny-based substitution models JO - Genetics VL - 193 ID - Rodrigue2013 ER - TY - JOUR AU - Doud, M. B. AU - Ashenberg, O. AU - Bloom, J. D. PY - 2015 DA - 2015// TI - Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs JO - Mol Biol Evol VL - 32 ID - Doud2015 ER - TY - JOUR AU - Parto, S. AU - Lartillot, N. PY - 2017 DA - 2017// TI - Detecting consistent patterns of directional adaptation using differential selection codon models JO - BMC Evol Biol VL - 17 ID - Parto2017 ER - TY - JOUR AU - Rodrigue, N. AU - Philippe, H. AU - Lartillot, N. PY - 2010 DA - 2010// TI - Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles JO - Proc Natl Acad Sci VL - 107 ID - Rodrigue2010 ER - TY - JOUR AU - Rodrigue, N. AU - Aris-Brosou, S. PY - 2011 DA - 2011// TI - Fast bayesian choice of phylogenetic models: Prospecting data augmentation–based thermodynamic integration JO - Syst Biol VL - 60 ID - Rodrigue2011 ER - TY - JOUR AU - Yang, Z. PY - 1993 DA - 1993// TI - Maximum-likelihood estimation of phylogeny from dna sequences when substitution rates differ over sites JO - Mol Biol Evol VL - 10 ID - Yang1993 ER - TY - JOUR AU - Yang, Z. PY - 1994 DA - 1994// TI - Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: approximate methods JO - J Mol Evol VL - 39 ID - Yang1994 ER - TY - JOUR AU - Nielsen, R. PY - 2002 DA - 2002// TI - Mapping mutations on phylogenies JO - Syst Biol VL - 51 ID - Nielsen2002 ER - TY - JOUR AU - Kosakovsky Pond, S. L. AU - Murrell, B. AU - Fourment, M. AU - Frost, S. D. AU - Delport, W. AU - Scheffler, K. PY - 2011 DA - 2011// TI - A random effects branch-site model for detecting episodic diversifying selection JO - Mol Biol Evol VL - 28 ID - Kosakovsky Pond2011 ER - TY - JOUR AU - Guindon, S. AU - Rodrigo, A. G. AU - Dyer, K. A. AU - Huelsenbeck, J. P. PY - 2004 DA - 2004// TI - Modeling the site-specific variation of selection patterns along lineages JO - Proc Natl Acad Sci VL - 101 ID - Guindon2004 ER - TY - JOUR AU - Quang, L. S. AU - Gascuel, O. AU - Lartillot, N. PY - 2008 DA - 2008// TI - Empirical profile mixture models for phylogenetic reconstruction JO - Bioinformatics VL - 24 ID - Quang2008 ER - TY - JOUR AU - Rodrigue, N. AU - Philippe, H. AU - Lartillot, N. PY - 2007 DA - 2007// TI - Exploring fast computational strategies for probabilistic phylogenetic analysis JO - Syst Biol VL - 56 ID - Rodrigue2007 ER - TY - STD TI - Robert C, Casella G. Introducing Monte Carlo Methods with R (Vol. 18).New York: Springer; 2010. p. 217. ID - ref29 ER - TY - JOUR AU - Tamuri, A. U. AU - dos Reis, M. AU - Hay, A. J. AU - Goldstein, R. A. PY - 2009 DA - 2009// TI - Identifying changes in selective constraints: host shifts in influenza JO - PLoS Comput Biol VL - 5 ID - Tamuri2009 ER - TY - JOUR AU - Lartillot, N. AU - Rodrigue, N. AU - Stubbs, D. AU - Richer, J. PY - 2013 DA - 2013// TI - Phylobayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment, JO - Syst Biol VL - 62 ID - Lartillot2013 ER - TY - JOUR AU - Rodrigue, N. AU - Lartillot, N. PY - 2014 DA - 2014// TI - Site-heterogeneous mutation-selection models within the phylobayes-mpi package JO - Bioinformatics VL - 30 ID - Rodrigue2014 ER - TY - JOUR AU - Le, S. Q. AU - Gascuel, O. PY - 2008 DA - 2008// TI - An improved general amino acid replacement matrix JO - Mol Biol Evol VL - 25 ID - Le2008 ER - TY - JOUR AU - Nielsen, R. AU - Bauer DuMont, V. L. AU - Hubisz, M. J. AU - Aquadro, C. F. PY - 2006 DA - 2006// TI - Maximum likelihood estimation of ancestral codon usage bias parameters in drosophila JO - Mol Biol Evol VL - 24 ID - Nielsen2006 ER - TY - JOUR AU - Platt, A. AU - Weber, C. C. AU - Liberles, D. A. PY - 2018 DA - 2018// TI - Protein evolution depends on multiple distinct population size parameters JO - BMC Evol Biol VL - 18 ID - Platt2018 ER - TY - JOUR AU - Rodrigue, N. AU - Lartillot, N. PY - 2017 DA - 2017// TI - Detecting adaptation in protein-coding genes using a bayesian site-heterogeneous mutation-selection codon substitution model JO - Mol Biol Evol VL - 34 ID - Rodrigue2017 ER - TY - JOUR AU - Bloom, J. D. PY - 2017 DA - 2017// TI - Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models JO - Biol Dir VL - 12 ID - Bloom2017 ER -