J. Adachi and M. Hasegawa, Model of amino acid substitution in proteins encoded by mitochondrial DNA, Journal of Molecular Evolution, vol.41, issue.4, pp.459-468, 1996.
DOI : 10.1007/BF02498640

J. Adachi, P. J. Waddell, W. Martin, and M. Hasegawa, Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA, Journal of Molecular Evolution, vol.50, issue.4, pp.348-358, 2000.
DOI : 10.1007/s002399910038

H. Akaike, A new look at the statistical model identification, IEEE Trans. Automat. Control, AC, issue.6, pp.19-716, 1974.

C. E. Antoniak, Mixtures of Dirichlet Processes with Applications to Bayesian Nonparametric Problems, The Annals of Statistics, vol.2, issue.6, pp.1152-1174, 1974.
DOI : 10.1214/aos/1176342871

H. Brinkmann, M. Van-der-giezen, Y. Zhou, G. Poncelin-de-raucourt, P. et al., An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics, Systematic Biology, vol.54, issue.5, pp.743-757, 2005.
DOI : 10.1080/10635150500234609

W. J. Bruno, Modeling residue usage in aligned protein sequences via maximum likelihood, Molecular Biology and Evolution, vol.13, issue.10, pp.1368-74, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025583

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

G. E. Crooks and S. E. Brenner, An alternative model of amino acid replacement, Bioinformatics, vol.21, issue.7, pp.975-980, 2005.
DOI : 10.1093/bioinformatics/bti109

M. Dayhoff, R. Schwartz, and B. Orcutt, A model of evolutionary change in proteins, Atlas of Protein Sequence and Structure, pp.345-352, 1978.

A. Dempster, N. Laird, R. , and D. , Maximum likelihood from incomplete data via the EM algorithm, J. R. Stat. Soc. B, vol.39, pp.1-38, 1997.

J. F. Dufayard, L. Duret, S. Penel, M. Gouy, F. et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-2603, 2005.
DOI : 10.1093/bioinformatics/bti325
URL : https://hal.archives-ouvertes.fr/hal-00427861

J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.24, issue.6, pp.368-376, 1981.
DOI : 10.1007/BF01734359

J. Felsenstein and G. A. Churchill, A Hidden Markov Model approach to variation among sites in rate of evolution, Molecular Biology and Evolution, vol.13, issue.1, pp.93-104, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025575

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

O. Gascuel and S. Guindon, Modelling the variability of evolutionary processes, Reconstructing Evolution: new mathematical and computational advances, pp.65-99, 2007.
URL : https://hal.archives-ouvertes.fr/lirmm-00171206

N. Goldman, J. L. Thorne, and D. T. Jones, Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses, Journal of Molecular Biology, vol.263, issue.2, pp.196-208, 1996.
DOI : 10.1006/jmbi.1996.0569

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

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

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

I. Holmes and G. M. Rubin, An expectation maximization algorithm for training hidden substitution models11Edited by F. Cohen, Journal of Molecular Biology, vol.317, issue.5, pp.753-764, 2002.
DOI : 10.1006/jmbi.2002.5405

W. Hordijk and O. Gascuel, Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood, Bioinformatics, vol.21, issue.24, pp.4338-4347, 2005.
DOI : 10.1093/bioinformatics/bti713
URL : https://hal.archives-ouvertes.fr/lirmm-00137439

J. P. Huelsenbeck and M. A. Suchard, A Nonparametric Method for Accommodating and Testing Across-Site Rate Variation, Systematic Biology, vol.56, issue.6, pp.975-987, 2007.
DOI : 10.1080/10635150701670569

J. P. Huelsenbeck, S. Jain, S. W. Frost, and S. L. Pond, A Dirichlet process model for detecting positive selection in protein-coding DNA sequences, Proceedings of the National Academy of Sciences, vol.103, issue.16, pp.6263-6268, 2006.
DOI : 10.1073/pnas.0508279103

D. T. Jones, W. R. Taylor, T. , and J. M. , The rapid generation of mutation data matrices from protein sequences, Bioinformatics, vol.8, issue.3, pp.275-282, 1992.
DOI : 10.1093/bioinformatics/8.3.275

P. J. Keeling and N. M. Fast, Microsporidia: Biology and Evolution of Highly Reduced Intracellular Parasites, Annual Review of Microbiology, vol.56, issue.1, pp.93-116, 2002.
DOI : 10.1146/annurev.micro.56.012302.160854

H. Kishino and M. Hasegawa, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea, Journal of Molecular Evolution, vol.46, issue.2, pp.170-179, 1989.
DOI : 10.1007/BF02100115

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

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.1095-1109, 2004.
DOI : 10.1093/molbev/msh112
URL : https://hal.archives-ouvertes.fr/lirmm-00108585

N. Lartillot and H. Philippe, Computing Bayes Factors Using Thermodynamic Integration, Systematic Biology, vol.55, issue.2, pp.195-207, 2006.
DOI : 10.1080/10635150500433722
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.408.7842

N. Lartillot, H. Brinkmann, P. , and H. , Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model, BMC Evolutionary Biology, vol.7, issue.Suppl 1, p.4, 2007.
DOI : 10.1186/1471-2148-7-S1-S4
URL : https://hal.archives-ouvertes.fr/lirmm-00135024

S. Q. Le and O. Gascuel, An Improved General Amino Acid Replacement Matrix, Molecular Biology and Evolution, vol.25, issue.7, pp.1307-1320, 2008.
DOI : 10.1093/molbev/msn067
URL : https://hal.archives-ouvertes.fr/lirmm-00324106

R. M. Neal, Markov chain sampling methods for Dirichlet process mixture models, J. Comput. Graph. Stat, vol.9, pp.249-265, 2000.
DOI : 10.1080/10618600.2000.10474879
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.115.3668

R. Nielsen, Mapping Mutations on Phylogenies, Systematic Biology, vol.51, issue.5, pp.729-739, 2002.
DOI : 10.1080/10635150290102393
URL : http://sysbio.oxfordjournals.org/cgi/content/short/51/5/729

M. Pagel and A. Meade, A phylogenetic mixture model for detecting patternheterogeneity in gene sequence or character-state data, Syst. Biol, vol.53, pp.561-581, 2004.

H. Philippe, N. Lartillot, and H. Brinkmann, Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia, Molecular Biology and Evolution, vol.22, issue.5, pp.1246-1253, 2005.
DOI : 10.1093/molbev/msi111
URL : https://hal.archives-ouvertes.fr/lirmm-00105354

C. Sander and R. Schneider, Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins: Structure, Function, and Genetics, vol.4, issue.1, pp.56-68, 1991.
DOI : 10.1002/prot.340090107

M. J. Sanderson, B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson et al., The Growth of Phylogenetic Information and the Need for a Phylogenetic Data Base, Systematic Biology, vol.42, issue.4, pp.562-568, 1993.
DOI : 10.1093/sysbio/42.4.562

G. Schwartz, Estimating the Dimension of a Model, The Annals of Statistics, vol.6, issue.2, pp.461-464, 1978.
DOI : 10.1214/aos/1176344136

H. Shimodaira and M. Hasegawa, Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference, Molecular Biology and Evolution, vol.16, issue.8, pp.1114-1116, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026201

M. Steel, Should phylogenetic models be trying to ???fit an elephant????, Trends in Genetics, vol.21, issue.6, pp.310-311, 2005.
DOI : 10.1016/j.tig.2005.04.001

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
URL : http://mbe.oxfordjournals.org/cgi/content/short/13/5/666

S. Whelan and N. Goldman, A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach, Molecular Biology and Evolution, vol.18, issue.5, pp.691-699, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003851

S. Whelan, P. Lio, and N. Goldman, Molecular phylogenetics: state-of-the-art methods for looking into the past, Trends in Genetics, vol.17, issue.5, pp.262-272, 2001.
DOI : 10.1016/S0168-9525(01)02272-7

Z. Yang, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods, Journal of Molecular Evolution, vol.11, issue.3, pp.306-320, 1994.
DOI : 10.1007/BF00160154
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.6626

Z. Yang, R. Nielsen, N. Goldman, and A. K. Pedersen, Codon-substitution models for heterogeneous selection pressure at amino-acid sites, Genetics, vol.155, pp.431-449, 2000.