F. Abascal, R. Zardoya, and D. Posada, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, issue.9, pp.2104-2105, 2005.
DOI : 10.1093/bioinformatics/bti263

B. L. Allen and M. Steel, Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees, Annals of Combinatorics, vol.5, issue.1, pp.1-15, 2001.
DOI : 10.1007/s00026-001-8006-8

J. M. Archibald and A. J. Roger, Gene Conversion and the Evolution of Euryarchaeal Chaperonins: A Maximum Likelihood-Based Method for Detecting Conflicting Phylogenetic Signals, Journal of Molecular Evolution, vol.55, issue.2, pp.232-245, 2002.
DOI : 10.1007/s00239-002-2321-5

C. K. Armitage, B. C. Mcpherson, and . Rowe, Repeated Significance Tests on Accumulating Data, Journal of the Royal Statistical Society. Series A (General), vol.132, issue.2, pp.235-244, 1969.
DOI : 10.2307/2343787

P. F. Arndt, C. B. Burge, and T. Hwa, Dna sequence evolution with neighbor-dependent mutation, J Comput Biol, vol.10, pp.3-4313, 2003.

A. Bar-hen and H. Kishino, Comparing the Likelihood Functions of Phylogenetic Trees, Annals of the Institute of Statistical Mathematics, vol.52, issue.1, pp.43-56, 2000.
DOI : 10.1023/A:1004180831122

A. Bar-hen, M. Mariadassou, M. Poursat, and P. Vandenkoornhuyse, Influence Function for Robust Phylogenetic Reconstructions, Molecular Biology and Evolution, vol.25, issue.5, pp.869-873, 2008.
DOI : 10.1093/molbev/msn030

URL : https://hal.archives-ouvertes.fr/hal-00312860

N. M. Belfiore, L. Liu, and C. Moritz, Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae), Systematic Biology, vol.57, issue.2, pp.294-310, 2008.
DOI : 10.1080/10635150802044011

G. Bello, C. Casado, S. García, C. Rodríguez, J. Del-romero et al., Lack of temporal structure in the short term HIV-1 evolution within asymptomatic na??ve patients, Virology, vol.362, issue.2, pp.294-303, 2007.
DOI : 10.1016/j.virol.2006.11.039

G. Bennett, Probability Inequalities for the Sum of Independent Random Variables, Journal of the American Statistical Association, vol.18, issue.297, pp.33-45, 1962.
DOI : 10.1214/aoms/1177730437

A. Benveniste, M. Basseville, and G. Moustakides, The asymptotic local approach to change detection and model validation, IEEE Transactions on Automatic Control, vol.32, issue.7, pp.583-592, 1987.
DOI : 10.1109/TAC.1987.1104683

URL : https://hal.archives-ouvertes.fr/inria-00075990

L. J. Billera, S. P. Holmes, and K. Vogtmann, Geometry of the Space of Phylogenetic Trees, Advances in Applied Mathematics, vol.27, issue.4, pp.733-767, 2001.
DOI : 10.1006/aama.2001.0759

S. Blanquart and N. Lartillot, A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution, Molecular Biology and Evolution, vol.23, issue.11, pp.2058-2071, 2006.
DOI : 10.1093/molbev/msl091

URL : https://hal.archives-ouvertes.fr/lirmm-00135037

S. Blanquart and N. Lartillot, A Site- and Time-Heterogeneous Model of Amino Acid Replacement, Molecular Biology and Evolution, vol.25, issue.5, pp.842-858, 2008.
DOI : 10.1093/molbev/msn018

URL : https://hal.archives-ouvertes.fr/lirmm-00324422

C. Blouin, D. Butt, and A. J. Roger, Impact of Taxon Sampling on the Estimation of Rates of Evolution at Sites, Molecular Biology and Evolution, vol.22, issue.3, pp.784-791, 2005.
DOI : 10.1093/molbev/msi065

M. Bordewich, A. G. Rodrigo, and C. Semple, Selecting Taxa to Save or Sequence: Desirable Criteria and a Greedy Solution, Systematic Biology, vol.57, issue.6, pp.825-834, 2008.
DOI : 10.1080/10635150802552831

B. Boussau and M. Gouy, Efficient Likelihood Computations with Nonreversible Models of Evolution, Systematic Biology, vol.55, issue.5, pp.756-768, 2006.
DOI : 10.1080/10635150600975218

URL : https://hal.archives-ouvertes.fr/hal-00427908

B. Brodsky and B. Darkovsky, Non-Parametric Statistical Diagnosis. Problems and Methods, 2000.

B. Brodsky and B. Darkovsky, Asymptotically optimal methods of change-point detection for composite hypotheses, Journal of Statistical Planning and Inference, vol.133, issue.1, pp.123-138, 2005.
DOI : 10.1016/j.jspi.2004.01.007

D. Bryant, N. Galtier, and M. A. Poursat, Mathematics of evolution and phylogeny, chapter Likelihood calculation in molecular phylogenetics, pp.33-62, 2005.

T. R. Buckley, Model Misspecification and Probabilistic Tests of Topology: Evidence from Empirical Data Sets, Systematic Biology, vol.51, issue.3, pp.509-523, 2002.
DOI : 10.1080/10635150290069922

J. Buschbom and A. Haeseler, Statistical Methods in Molecular Evolution, chapter Introduction to Applications of the Likelihood Function in Molecular Evolution, pp.25-44, 2004.

R. M. Bush, C. A. Bender, K. Subbarao, N. J. Cox, and W. M. Fitch, Predicting the Evolution of Human Influenza A, Science, vol.286, issue.5446, pp.2861921-1925, 1999.
DOI : 10.1126/science.286.5446.1921

J. Bérard, J. Gouéré, and D. Piau, Solvable models of neighbor-dependent substitution processes, Mathematical Biosciences, vol.211, issue.1, pp.56-88, 2008.
DOI : 10.1016/j.mbs.2007.10.001

Y. Cao, J. Adachi, T. Yano, and M. Hasegawa, Phylogenetic place of guinea pigs: no support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences, Mol Biol Evol, vol.11, issue.4, pp.593-604, 1994.

Y. Cao, N. Okada, and M. Hasegawa, Phylogenetic position of guinea pigs revisited, Molecular Biology and Evolution, vol.14, issue.4, pp.461-464, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025782

L. L. Cavalli-sforza and A. W. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.233-257, 1967.
DOI : 10.2307/2406616

A. Chao, Nonparametric estimation of the number of classes in a population, Scand. J. Statis, vol.11, pp.265-270, 1984.

R. D. Cook, Influential Observations in Linear Regression, Journal of the American Statistical Association, vol.2, issue.365, pp.169-174, 1979.
DOI : 10.1080/01621459.1979.10481634

H. Cramer, Random Variables and Probability Distributions, Cambrige Tracts in Mathematics, vol.36, 1937.

K. A. Cranston and B. Rannala, Summarizing a Posterior Distribution of Trees Using Agreement Subtrees, Systematic Biology, vol.56, issue.4, pp.578-590, 2007.
DOI : 10.1080/10635150701485091

A. Cuevas and J. Romo, On the estimation of the influence curve, Canadian Journal of Statistics, vol.18, issue.1, pp.1-9, 1995.
DOI : 10.2307/3315546

C. Darwin, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, 1859.

A. M. D-'erchia, C. Gissi, G. Pesole, C. Saccone, and U. Arnason, The guinea-pig is not a rodent, Nature, issue.6583, pp.381597-600, 1996.

P. Domingos and G. Hulten, Mining high-speed data streams, Proceedings of the sixth ACM SIGKDD international conference on Knowledge discovery and data mining , KDD '00, pp.71-80, 2000.
DOI : 10.1145/347090.347107

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.119.3124

C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne et al., Broad phylogenomic sampling improves resolution of the animal tree of life, Nature, vol.22, issue.7188, pp.452745-749, 2008.
DOI : 10.1038/nature06614

L. Duret, The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana, Journal of Molecular Evolution, vol.20, issue.6, pp.803-806, 2006.
DOI : 10.1007/s00239-005-0228-7

URL : https://hal.archives-ouvertes.fr/hal-00427950

L. Duret, Neutral theory: The nulll hypothesis of molecular evolution, Nature Education, vol.1, issue.1, 2008.

L. Duret and N. Galtier, The Covariation Between TpA Deficiency, CpG Deficiency, and G+C Content of Human Isochores Is Due to a Mathematical Artifact, Molecular Biology and Evolution, vol.17, issue.11, pp.1620-1625, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026261

URL : https://hal.archives-ouvertes.fr/hal-00427077

A. W. Edwards, Estimation of the branch points of a branching diffiasion process (with discussion), J. R. Stat. Soc. B, vol.32, pp.155-174, 1970.

A. W. Edwards and L. L. Cavalli-sforza, The reconstruction of evolution, Annals of Human Genetics, vol.27, pp.105-106, 1963.

A. W. Edwards and L. L. Cavalli-sforza, Phenetic and Phylogenetic Classification, chapter Reconstruction of evolutionary trees, Systematics Association Publ, issue.6, pp.67-76, 1964.

B. Efron, Bootstrap Methods: Another Look at the Jackknife, The Annals of Statistics, vol.7, issue.1, pp.1-26, 1979.
DOI : 10.1214/aos/1176344552

B. Efron, E. Halloran, and S. Holmes, Bootstrap confidence levels for phylogenetic trees., Proceedings of the National Academy of Sciences, vol.93, issue.14, pp.7085-7090, 1996.
DOI : 10.1073/pnas.93.14.7085

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24110

J. A. Eisen, Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary???Analysis, Genome Research, vol.8, issue.3, pp.163-167, 1998.
DOI : 10.1101/gr.8.3.163

J. A. Eisen and M. Wu, Phylogenetic Analysis and Gene Functional Predictions: Phylogenomics in Action, Theoretical Population Biology, vol.61, issue.4, pp.481-487, 2002.
DOI : 10.1006/tpbi.2002.1594

C. Esseen, Fourier analysis of distribution functions. A mathematical study of the Laplace-Gaussian law, Acta Mathematica, vol.77, issue.0, pp.1-125, 1945.
DOI : 10.1007/BF02392223

M. Falconnet, Phylogenetic distances for neighbour dependent substitution processes, Mathematical Biosciences, vol.224, issue.2, 1962.
DOI : 10.1016/j.mbs.2009.12.010

URL : https://hal.archives-ouvertes.fr/hal-00345897

J. Farris, Advances in Cladistics, chapter The Logical Basis of Phylogenetic Analysis, pp.7-36, 1983.

J. Felsenstein, Statistical Inference and the Estimation of Phylogenies, 1968.

J. Felsenstein, Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters, Systematic Zoology, vol.22, issue.3, pp.240-249, 1973.
DOI : 10.2307/2412304

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

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, Confidence Limits on Phylogenies: An Approach Using the Bootstrap, Evolution, vol.39, issue.4, pp.783-791, 1985.
DOI : 10.2307/2408678

J. Felsenstein, Phylip (phylogeny inference package) version 3.6. Distributed by the author, 2005.

J. Felsenstein and H. Kishino, Is there Something Wrong with the Bootstrap on Phylogenies? A Reply to Hillis and Bull, Systematic Biology, vol.42, issue.2, pp.193-200, 1993.
DOI : 10.1093/sysbio/42.2.193

J. Felsentstein, Statistical inference of phylogenies, J.R. Statist. Soc, vol.146, issue.3, pp.246-272, 1983.

R. A. Fisher, XV.???The Correlation between Relatives on the Supposition of Mendelian Inheritance., Transactions of the Royal Society of Edinburgh, vol.ii, issue.02, pp.399-433, 1918.
DOI : 10.1017/S0080456800012163

W. M. Fitch and E. Margoliash, Construction of Phylogenetic Trees, Science, vol.155, issue.3760, pp.279-284, 1967.
DOI : 10.1126/science.155.3760.279

N. Galtier, Maximum-Likelihood Phylogenetic Analysis Under a Covarion-like Model, Molecular Biology and Evolution, vol.18, issue.5, pp.866-873, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003868

N. Galtier and L. Duret, Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution, Trends in Genetics, vol.23, issue.6, pp.273-277, 2007.
DOI : 10.1016/j.tig.2007.03.011

URL : https://hal.archives-ouvertes.fr/halsde-00424420

O. Gascuel, Mathematics of evolution and phylogeny, 2005.
URL : https://hal.archives-ouvertes.fr/lirmm-00185867

J. Gatesy, R. Desalle, and N. Wahlberg, How Many Genes Should a Systematist Sample? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence, Systematic Biology, vol.56, issue.2, pp.355-363, 2007.
DOI : 10.1080/10635150701294733

K. Geuten, T. Massingham, P. Darius, E. Smets, and N. Goldman, Experimental Design Criteria in Phylogenetics: Where to Add Taxa, Systematic Biology, vol.56, issue.4, pp.609-622, 2007.
DOI : 10.1080/10635150701499563

A. L. Gibbs and E. Su, On Choosing and Bounding Probability Metrics, International Statistical Review, vol.28, issue.2, pp.419-435, 2002.
DOI : 10.1111/j.1751-5823.2002.tb00178.x

N. Goldman, Simple diagnostic statistical tests of models for DNA substitution, Journal of Molecular Evolution, vol.37, issue.6, pp.650-661, 1993.
DOI : 10.1007/BF00182751

N. Goldman, Statistical tests of models of DNA substitution, Journal of Molecular Evolution, vol.46, issue.2, pp.182-198, 1993.
DOI : 10.1007/BF00166252

N. Goldman, Phylogenetic information and experimental design in molecular systematics, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1407, pp.1779-1786, 1407.
DOI : 10.1098/rspb.1998.0502

N. Goldman, J. P. Anderson, and A. G. Rodrigo, Likelihood-Based Tests of Topologies in Phylogenetics, Systematic Biology, vol.49, issue.4, pp.652-670, 2000.
DOI : 10.1080/106351500750049752

D. Graur, W. A. Hide, and W. H. Li, Is the guinea-pig a rodent?, Nature, vol.351, issue.6328, pp.649-652, 1991.
DOI : 10.1038/351649a0

I. Gronau, S. Moran, and S. Snir, Fast and Reliable Reconstruction of Phylogenetic Trees with Very Short Edges, SODA: ACM-SIAM Symposium on Discrete Algorithms, pp.379-388, 2008.

X. Gu, Maximum-Likelihood Approach for Gene Family Evolution Under Functional Divergence, Molecular Biology and Evolution, vol.18, issue.4, pp.453-464, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003824

X. Gu, Statistical Framework for Phylogenomic Analysis of Gene Family Expression Profiles, Genetics, vol.167, issue.1, pp.531-542, 2004.
DOI : 10.1534/genetics.167.1.531

X. Gu, A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences, Molecular Biology and Evolution, vol.23, issue.10, pp.1937-1945, 2006.
DOI : 10.1093/molbev/msl056

X. Gu, Z. Zhang, and W. Huang, Rapid evolution of expression and regulatory divergences after yeast gene duplication, Proceedings of the National Academy of Sciences, vol.102, issue.3, pp.707-712, 2005.
DOI : 10.1073/pnas.0409186102

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

H. Guo, R. E. Weiss, X. Gu, and M. A. Suchard, Time Squared: Repeated Measures on Phylogenies, Molecular Biology and Evolution, vol.24, issue.2, pp.352-362, 2007.
DOI : 10.1093/molbev/msl165

P. Hall, Bootstrap and Edgeworth Expansion, 1984.
DOI : 10.1007/978-1-4612-4384-7

F. R. Hampel, The Influence Curve and its Role in Robust Estimation, Journal of the American Statistical Association, vol.15, issue.4, pp.383-393, 1974.
DOI : 10.1214/aoms/1177730385

F. R. Hampel, The Influence Curve and its Role in Robust Estimation, Journal of the American Statistical Association, vol.15, issue.4, pp.383-393, 1974.
DOI : 10.1214/aoms/1177730385

M. Hasegawa and M. Fujiwara, Relative Efficiencies of the Maximum Likelihood, Maximum Parsimony, and Neighbor-Joining Methods for Estimating Protein Phylogeny, Molecular Phylogenetics and Evolution, vol.2, issue.1, pp.1-5, 1993.
DOI : 10.1006/mpev.1993.1001

M. Hasegawa and H. Kishino, Confidence Limits of the Maximum-Likelihood Estimate of the Hominoid three from Mitochondrial-DNA Sequences, Evolution, vol.43, issue.3, pp.672-677, 1989.
DOI : 10.2307/2409071

M. Hasegawa and H. Kishino, Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree, Mol Biol Evol, vol.11, pp.142-145, 1994.

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985.
DOI : 10.1007/BF02101694

T. A. Heath, S. M. Hedtke, and D. M. Hillis, Taxon sampling and the accuracy of phylogenetic analyses, J Mol Evol, vol.46, pp.239-257, 2008.

P. D. Hebert, A. Cywinska, S. L. Ball, and J. R. Dewaard, Biological identifications through DNA barcodes, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1512, pp.313-321, 1512.
DOI : 10.1098/rspb.2002.2218

S. M. Hedtke, T. M. Townsend, and D. M. Hillis, Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling, Systematic Biology, vol.55, issue.3, pp.522-529, 2006.
DOI : 10.1080/10635150600697358

D. M. Hillis and J. J. Bull, An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis, Systematic Biology, vol.42, issue.2, pp.182-192, 1993.
DOI : 10.1093/sysbio/42.2.182

D. M. Hillis, D. D. Pollock, J. A. Mcguire, and D. J. , Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?, Systematic Biology, vol.52, issue.1, pp.124-126, 2003.
DOI : 10.1080/10635150390132911

W. Hoeffding, Probability Inequalities for Sums of Bounded Random Variables, Journal of the American Statistical Association, vol.1, issue.301, pp.13-30, 1963.
DOI : 10.1214/aoms/1177730491

B. R. Holland, D. Penny, and M. D. Hendy, Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock--A Simulation Study, Systematic Biology, vol.52, issue.2, pp.229-238, 2003.
DOI : 10.1080/10635150390192771

S. Holmes, Mathematics of evolution and phylogeny, chapter Statistical approach to tests involving phylogenies, pp.91-120, 2005.

S. Holmes, Bootstrapping Phylogenetic Trees: Theory and Methods, Statistical Science, vol.18, issue.2, pp.241-255, 2003.
DOI : 10.1214/ss/1063994979

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.550.9417

P. J. Huber, Robust Statistics, 1981.
DOI : 10.1002/0471725250

P. J. Huber, Robust Statistics, 2004.

J. P. Huelsenbeck, Testing a Covariotide Model of DNA Substitution, Molecular Biology and Evolution, vol.19, issue.5, pp.698-707, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004128

J. P. Huelsenbeck and J. P. Bollback, Handbook of Statistical Genetics, 3rd Edition, chapter Application of the Likelihood Function in Phylogenetic Analysis, pp.460-488, 2007.

A. J. Jeffreys, V. Wilson, and S. L. Thein, Hypervariable ???minisatellite??? regions in human DNA, Nature, vol.12, issue.6006, pp.31467-73, 1985.
DOI : 10.1038/314067a0

D. T. Jones, W. R. Taylor, and J. M. Thornton, 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. Jonniaux and Y. Kumazawa, Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae), Gene, vol.407, issue.1-2, pp.105-115, 2008.
DOI : 10.1016/j.gene.2007.09.023

T. Jukes and C. Cantor, Evolution of Protein Molecules, pp.21-132, 1969.
DOI : 10.1016/B978-1-4832-3211-9.50009-7

M. G. Kendall and A. Stuart, The advanced theory of statistics, 1973.

J. Kim, Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators, Systematic Biology, vol.47, issue.1, pp.43-60, 1998.
DOI : 10.1080/106351598261021

J. Kim, Slicing Hyperdimensional Oranges: The Geometry of Phylogenetic Estimation, Molecular Phylogenetics and Evolution, vol.17, issue.1, pp.58-75, 2000.
DOI : 10.1006/mpev.2000.0816

M. Kimura, Evolutionary Rate at the Molecular Level, Nature, vol.16, issue.5129, pp.624-626, 1968.
DOI : 10.1038/217624a0

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1007/BF01731581

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

Y. Kitazoe, H. Kishino, P. J. Waddell, N. Nakajima, T. Okabayashi et al., Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals, PLoS ONE, vol.2, issue.4, p.384, 2007.
DOI : 10.1371/journal.pone.0000384.s005

M. K. Kuhner and J. Felsenstein, A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol Biol Evol, vol.11, issue.3, pp.459-468, 1994.

S. Kullback and R. A. Leibler, On Information and Sufficiency, The Annals of Mathematical Statistics, vol.22, issue.1, pp.79-86, 1951.
DOI : 10.1214/aoms/1177729694

H. R. Künsch, The Jackknife and the Bootstrap for General Stationary Observations, The Annals of Statistics, vol.17, issue.3, pp.1217-1241, 1989.
DOI : 10.1214/aos/1176347265

S. N. Lahiri, Theoretical comparisons of block bootstrap methods. The Annals of Statistics, pp.386-404, 1999.

T. L. Lai, Sequential changepoint detection in quality control and dynamical systems (with discussion), J. Roy. Statist. Soc. Ser. B, vol.57, pp.613-658, 1995.

T. L. Lai and J. Z. Shan, Efficient recursive algorithms for detection of abrupt changes in signals and systems, IEEE Trans. Automatic Control, vol.44, pp.952-966, 1999.

C. Lanave, G. Preparata, C. Saccone, and G. Serio, A new method for calculating evolutionary substitution rates, Journal of Molecular Evolution, vol.46, issue.1, pp.86-93, 1984.
DOI : 10.1007/BF02101990

S. M. Lanyon, Detecting Internal Inconsistencies in Distance Data, Systematic Zoology, vol.34, issue.4, pp.397-403, 1985.
DOI : 10.2307/2413204

. Larson, Evolution: The Remarkable History of a Scientific Theory. Modern Library, 2006.

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, H. Brinkmann, and H. Philippe, 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

G. Lecointre, H. Philippe, H. L. Lê, and H. L. Guyader, Species Sampling Has a Major Impact on Phylogenetic Inference, Molecular Phylogenetics and Evolution, vol.2, issue.3, pp.205-224, 1993.
DOI : 10.1006/mpev.1993.1021

C. Li, G. Lu, and G. Orti, Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci, Systematic Biology, vol.57, issue.4, pp.519-539, 2008.
DOI : 10.1080/10635150802206883

S. Li, Phylogenetic Tree Construction Using Markov Chain Monte Carlo, Journal of the American Statistical Association, vol.9, issue.450, 1996.
DOI : 10.1007/BF00161173

K. Liu, S. Raghavan, S. Nelesen, C. R. Linder, and T. Warnow, Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees, Science, vol.324, issue.5934, pp.3241561-1564, 2009.
DOI : 10.1126/science.1171243

C. X. Mao and B. G. Lindsay, Estimating the number of classes. The Annals of Statistics, pp.917-930, 2007.

P. Massart, Concentration inequalities and model selection, 2006.

F. A. Matsen and M. Steel, Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology, Systematic Biology, vol.56, issue.5, 2007.
DOI : 10.1080/10635150701627304

F. A. Matsen, E. Mossel, and M. Steel, Mixed-up Trees: the Structure of Phylogenetic Mixtures, Bulletin of Mathematical Biology, vol.14, issue.2, 2007.
DOI : 10.1007/s11538-007-9293-y

B. Mau, Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods, Biometrics, vol.14, issue.1, 1996.
DOI : 10.1006/tpbi.1994.1023

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.139.498

C. D. Michener and R. R. Sokal, A Quantitative Approach to a Problem in Classification, Evolution, vol.11, issue.2, pp.130-162, 1957.
DOI : 10.2307/2406046

R. G. Miller, The jackknife ? A review, Biometrika, vol.61, issue.1, pp.1-15, 1974.

E. Mossel and M. Steel, Mathematics Of Evolution And Phylogeny, chapter How much can evolved characters tell us about the tree that generated them?, pp.384-312, 2005.

M. Newton, Bootstrapping phylogenies: Large deviations and dispersion effects, Biometrika, vol.83, issue.2, pp.315-358, 1996.
DOI : 10.1093/biomet/83.2.315

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.127.6097

R. Nielsen, Statistical Methods in Molecular Evolution, Statistics for Biology and Health, 2004.
DOI : 10.1007/0-387-27733-1

E. Nowak and A. Bar-hen, Influence function and correspondence analysis, Journal of Statistical Planning and Inference, vol.134, issue.1, pp.26-35, 2005.
DOI : 10.1016/j.jspi.2004.02.013

P. C. O-'brien and T. R. Fleming, A Multiple Testing Procedure for Clinical Trials, Biometrics, vol.35, issue.3, pp.549-556, 1979.
DOI : 10.2307/2530245

R. Ota, P. J. Waddell, M. Hasegawa, H. Shimodaira, and H. Kishino, Appropriate Likelihood Ratio Tests and Marginal Distributions for Evolutionary Tree Models with Constraints on Parameters, Molecular Biology and Evolution, vol.17, issue.5, pp.798-803, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026358

S. P. Otto, M. P. Cummings, and J. Wakeley, New Uses for New Phylogenies, chapter Inferring phylogenies from DNA sequence data: the effects of sampling, 1996.

E. S. Page, CONTINUOUS INSPECTION SCHEMES, Biometrika, vol.41, issue.1-2, pp.100-114, 1954.
DOI : 10.1093/biomet/41.1-2.100

B. Papp, C. Pál, and L. D. Hurst, Evolution of cis-regulatory elements in duplicated genes of yeast, Trends in Genetics, vol.19, issue.8, pp.417-422, 2003.
DOI : 10.1016/S0168-9525(03)00174-4

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

F. Pazos and A. Valencia, Similarity of phylogenetic trees as indicator of protein-protein interaction, Protein Engineering Design and Selection, vol.14, issue.9, pp.609-614, 2001.
DOI : 10.1093/protein/14.9.609

J. Pearl, Reverend bayes on inference engines: A distributed hierarchical approach, AAAI-82 Proceedings, 1982.

D. Penny and M. Hendy, Estimating the reliability of evolutionary trees, Molecular Biology and Evolution, vol.3, pp.403-417, 1986.

D. Penny and M. D. Hendy, The Use of Tree Comparison Metrics, Systematic Zoology, vol.34, issue.1, pp.75-82, 1985.
DOI : 10.2307/2413347

D. Penny, M. Hendy, and M. Steel, Progress with methods for constructing evolutionary trees, Trends in Ecology & Evolution, vol.7, issue.3, pp.73-79, 1992.
DOI : 10.1016/0169-5347(92)90244-6

H. Philippe, Rodent monophyly: pitfalls of molecular phylogenies, J Mol Evol, vol.45, issue.6, pp.712-715, 1997.

S. J. Pocock, Group sequential methods in the design and analysis of clinical trials, Biometrika, vol.64, issue.2, pp.191-199, 1977.
DOI : 10.1093/biomet/64.2.191

. Poe, Evaluation of the Strategy of Long-Branch Subdivision to Improve the Accuracy of Phylogenetic Methods, Systematic Biology, vol.52, issue.3, pp.423-428, 2003.
DOI : 10.1080/10635150390197046

S. Poe and D. L. Swofford, Taxon sampling revisited, Nature, vol.383, issue.6725, pp.299-300, 1999.
DOI : 10.1038/18592

D. D. Pollock, D. J. Zwickl, J. A. Mcguire, and D. M. Hillis, Increased Taxon Sampling Is Advantageous for Phylogenetic Inference, Systematic Biology, vol.51, issue.4, pp.664-671, 2002.
DOI : 10.1080/10635150290102357

D. Posada and T. R. Buckley, Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests, Systematic Biology, vol.53, issue.5, pp.793-808, 2004.
DOI : 10.1080/10635150490522304

D. Posada and K. A. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

A. B. Prasad, M. W. Allard, N. I. Program, and E. D. Green, Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets, Molecular Biology and Evolution, vol.25, issue.9, pp.1795-1808, 2008.
DOI : 10.1093/molbev/msn104

B. Rannala and Z. Yang, Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference, Journal of Molecular Evolution, vol.9, issue.3, pp.304-311, 1996.
DOI : 10.1007/BF02338839

B. Rannala, J. P. Huelsenbeck, Z. Yang, and R. Nielsen, Taxon Sampling and the Accuracy of Large Phylogenies, Systematic Biology, vol.47, issue.4, pp.702-710, 1998.
DOI : 10.1080/106351598260680

D. F. Robinson and L. R. Foulds, Lectures Note in mathematics, pp.119-126, 1979.

A. Rokas and S. B. Carroll, More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy, Molecular Biology and Evolution, vol.22, issue.5, pp.1337-1344, 2005.
DOI : 10.1093/molbev/msi121

A. Rokas, B. L. Williams, N. King, and S. B. Carroll, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.425, issue.6960, pp.425798-804, 2003.
DOI : 10.1038/nature02053

F. Ronquist and J. P. Huelsenbeck, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1574, 2003.
DOI : 10.1093/bioinformatics/btg180

M. S. Rosenberg and S. Kumar, Incomplete taxon sampling is not a problem for phylogenetic inference, Proceedings of the National Academy of Sciences, vol.98, issue.19, pp.10751-10756, 2001.
DOI : 10.1073/pnas.191248498

T. Sato, Y. Yamanishi, K. Horimoto, M. Kanehisa, and H. Toh, Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions, Bioinformatics, vol.22, issue.20, pp.222488-2492, 2006.
DOI : 10.1093/bioinformatics/btl419

S. G. Self and K. Liang, Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions, Journal of the American Statistical Association, vol.72, issue.398, pp.605-610, 1987.
DOI : 10.1080/01621459.1987.10478472

L. Shavit, D. Penny, M. D. Hendy, and B. R. Holland, The Problem of Rooting Rapid Radiations, Molecular Biology and Evolution, vol.24, issue.11, pp.2400-2411, 2007.
DOI : 10.1093/molbev/msm178

H. Shimodaira, An Approximately Unbiased Test of Phylogenetic Tree Selection, Systematic Biology, vol.51, issue.3, pp.492-508, 2002.
DOI : 10.1080/10635150290069913

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

A. Siepel and D. Haussler, Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood, Molecular Biology and Evolution, vol.21, issue.3, pp.468-488, 2004.
DOI : 10.1093/molbev/msh039

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

M. A. Steel and L. A. Szekely, Inverting random functions, Annals of Combinatorics, vol.14, issue.1, pp.103-113, 1999.
DOI : 10.1007/BF01609880

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.110.7300

M. A. Steel and L. A. Szekely, Inverting Random Functions II: Explicit Bounds for Discrete Maximum Likelihood Estimation, with Applications, SIAM Journal on Discrete Mathematics, vol.15, issue.4, pp.562-575, 2002.
DOI : 10.1137/S089548010138790X

M. A. Steel and L. A. Szekely, Inverting Random Functions III: Discrete MLE Revisited, Annals of Combinatorics, vol.42, issue.3, 2006.
DOI : 10.1007/s00026-009-0023-z

M. A. Steel and L. A. Szekely, On the variational distance of two trees, The Annals of Applied Probability, vol.16, issue.3, pp.1563-1575, 2006.
DOI : 10.1214/105051606000000196

K. Strimmer and A. Rambaut, Inferring confidence sets of possibly misspecified gene trees, Proceedings of the Royal Society B: Biological Sciences, vol.269, issue.1487, pp.137-142, 1487.
DOI : 10.1098/rspb.2001.1862

. Study, The beta-blocker heart attack trial. beta-blocker heart attack study group, JAMA, vol.246, issue.18, pp.2073-2074, 1981.

J. Sullivan and D. L. Swofford, Are guinea pigs rodents? the importance of adequate models in molecular phylogenetics, Journal of Mammalian Evolution, vol.4, issue.2, pp.77-96, 1997.
DOI : 10.1023/A:1027314112438

E. Susko, Bootstrap Support Is Not First-Order Correct, Systematic Biology, vol.58, issue.2, 2009.
DOI : 10.1093/sysbio/syp016

D. L. Swofford, PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.04beta, 2003.

Y. Tang, A Hoeffding-Type Inequality for Ergodic Time Series, Journal of Theoretical Probability, vol.4, issue.2, pp.167-176, 2007.
DOI : 10.1007/s10959-007-0057-2

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

W. Thorley, Testing the Phylogenetic Stability of Early Tetrapods, Journal of Theoretical Biology, vol.200, issue.3, pp.343-344, 1999.
DOI : 10.1006/jtbi.1999.0999

C. Tuffley and M. Steel, Modeling the covarion hypothesis of nucleotide substitution, Mathematical Biosciences, vol.147, issue.1, pp.63-91, 1997.
DOI : 10.1016/S0025-5564(97)00081-3

S. Van-de-geer, Empirical Process Techniques for Dependent Data, chapter On Hoeffding's inequality for dependent random variables, pp.161-170, 2002.

P. Vandenkoornhuyse, S. L. Baldauf, C. Leyval, J. Straczek, and J. P. Young, Extensive Fungal Diversity in Plant Roots, Science, vol.295, issue.5562, p.2051, 2002.
DOI : 10.1126/science.295.5562.2051

J. D. Watson and F. Crick, MOLECULAR STRUCTURE OF NUCLEIC ACIDS, JAMA, vol.269, issue.15, pp.737-738, 1953.
DOI : 10.1001/jama.1993.03500150078030

M. Wilkinson, Majority-rule reduced consensus trees and their use in bootstrapping, Molecular Biology and Evolution, vol.13, issue.3, pp.437-444, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025604

S. Wuchty, Evolution and Topology in the Yeast Protein Interaction Network, Genome Research, vol.14, issue.7, pp.1310-1314, 2004.
DOI : 10.1101/gr.2300204

Z. Yang, Maximum-likelihood estimation of phylogeny from dna sequences when substitution rates differ over sites, Mol Biol Evol, vol.10, issue.6, pp.1396-1401, 1993.

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.306-314, 1994.
DOI : 10.1007/BF00160154

Z. Yang, Complexity of the simplest phylogenetic estimation problem, Proceedings of the Royal Society B: Biological Sciences, vol.267, issue.1439, pp.109-116, 2000.
DOI : 10.1098/rspb.2000.0974

Z. Yang, Fair-Balance Paradox, Star-tree Paradox, and Bayesian Phylogenetics, Molecular Biology and Evolution, vol.24, issue.8, pp.1639-1655, 2007.
DOI : 10.1093/molbev/msm081

URL : http://mbe.oxfordjournals.org/cgi/content/short/24/8/1639

Z. Yang, Estimating the pattern of nucleotide substitution, Journal of Molecular Evolution, vol.39, issue.1, pp.105-111, 1994.
DOI : 10.1007/BF00178256

Z. Yang, N. Goldman, and A. Friday, Maximum Likelihood Trees from DNA Sequences: A Peculiar Statistical Estimation Problem, Systematic Biology, vol.44, issue.3, pp.384-399, 1995.
DOI : 10.1093/sysbio/44.3.384

Z. Yang, R. Nielsen, and M. Hasegawa, Models of amino acid substitution and applications to mitochondrial protein evolution, Molecular Biology and Evolution, vol.15, issue.12, pp.1600-1611, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025888

H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia et al., Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs, Genome Research, vol.14, issue.6, pp.141107-1118, 2004.
DOI : 10.1101/gr.1774904

A. Zharkikh and W. H. Li, Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock, Journal of Molecular Evolution, vol.5, issue.4, pp.1119-1147, 1992.
DOI : 10.1007/BF00161173