S. L. Baldauf, A. J. Roger, I. Wenk-siefert, and W. F. Doolittle, A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data, Science, vol.290, issue.5493, pp.972-977, 2000.
DOI : 10.1126/science.290.5493.972

W. J. Bruno, Modeling residue usage in aligned protein sequences via maximum likelihood, Molecular Biology and Evolution, vol.13, issue.10, pp.1368-1374, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025583

M. W. Dimmic, D. P. Mindell, and R. A. Goldstein, MODELING EVOLUTION AT THE PROTEIN LEVEL USING AN ADJUSTABLE AMINO ACID FITNESS MODEL, Biocomputing 2000, pp.18-29, 2000.
DOI : 10.1142/9789814447331_0003

J. Felsenstein, Cases in which Parsimony or Compatibility Methods Will be Positively Misleading, Systematic Zoology, vol.27, issue.4, pp.401-410, 1978.
DOI : 10.2307/2412923

T. Ferguson, A Bayesian Analysis of Some Nonparametric Problems, The Annals of Statistics, vol.1, issue.2, pp.209-230, 1973.
DOI : 10.1214/aos/1176342360

N. Goldman, J. L. Thorne, and D. Jones, Assessing the impact of secondary structure and solvent accessiblity on protein evolution, Genetics, vol.149, pp.445-458, 1998.

P. J. Green and S. Richardson, Modelling Heterogeneity With and Without the Dirichlet Process, Scandinavian Journal of Statistics, vol.28, issue.2, 1998.
DOI : 10.1111/1467-9469.00242

A. L. Halpern and W. J. Bruno, Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies, Molecular Biology and Evolution, vol.15, issue.7, pp.910-917, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025995

D. Higgins, J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins et al., Clustal W : improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice, Nucleic Acids Res, vol.22, pp.4673-4680, 1994.

J. P. Huelsenbeck, B. Larget, R. E. Miller, and F. Ronquist, Potential applications and pitfalls of Bayesian inference of phylogeny, Syst. Biol, vol.51, pp.673-688, 2002.

J. P. Huelsenbeck and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, issue.8, pp.754-755, 2001.
DOI : 10.1093/bioinformatics/17.8.754

H. Jeffreys, Some Tests of Significance, Treated by the Theory of Probability, Proc. Camb, pp.203-222, 1935.
DOI : 10.1017/S030500410001330X

J. M. Koshi and R. A. Goldstein, Models of natural mutations including site heterogeneity, Proteins: Structure, Function, and Genetics, vol.3, issue.3, pp.289-295, 1998.
DOI : 10.1002/(SICI)1097-0134(19980815)32:3<289::AID-PROT4>3.0.CO;2-D

J. M. Koshi and R. A. Goldstein, Analysing site heterogeneity during protein evolution, Pac. Symp. Biocomput, vol.6, pp.191-202, 2001.

B. Larget and D. Simon, Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees, Molecular Biology and Evolution, vol.16, issue.6, pp.750-759, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026160

N. Lartillot and H. Philippe, A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process, Molecular Biology and Evolution, vol.21, issue.6, pp.1096-1109, 2004.
DOI : 10.1093/molbev/msh112

URL : https://hal.archives-ouvertes.fr/lirmm-00108585

R. M. Neal, Markov chain sampling methods for Dirichlet process mixture models, J. Comput. Graphical. Stat, vol.9, pp.249-265, 2000.
DOI : 10.2307/1390653

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

Y. Ogata, A Monte Carlo method for high dimensional integration, Numerische Mathematik, vol.28, issue.2, pp.137-157, 1989.
DOI : 10.1007/BF01406511

J. Sullivan and D. L. Swofford, Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site variations and nucleotide substitution pattern are violated ?, Syst. Biol, vol.50, pp.723-729, 2001.

J. L. Thorne, N. Goldman, and D. T. Jones, Combining protein evolution and secondary structure, Molecular Biology and Evolution, vol.13, issue.5, pp.666-673, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025627

A. Wald, Note on the Consistency of the Maximum Likelihood Estimate, The Annals of Mathematical Statistics, vol.20, issue.4, pp.595-601, 1949.
DOI : 10.1214/aoms/1177729952

Z. Yang, Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites, Mol. Biol. Evol, vol.10, pp.1396-1401, 1993.