ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, issue.9, pp.2104-2105, 2005. ,
DOI : 10.1093/bioinformatics/bti263
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
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
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
Dna sequence evolution with neighbor-dependent mutation, J Comput Biol, vol.10, pp.3-4313, 2003. ,
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
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
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
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
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
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
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
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
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
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
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
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
Non-Parametric Statistical Diagnosis. Problems and Methods, 2000. ,
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
Mathematics of evolution and phylogeny, chapter Likelihood calculation in molecular phylogenetics, pp.33-62, 2005. ,
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
Statistical Methods in Molecular Evolution, chapter Introduction to Applications of the Likelihood Function in Molecular Evolution, pp.25-44, 2004. ,
Predicting the Evolution of Human Influenza A, Science, vol.286, issue.5446, pp.2861921-1925, 1999. ,
DOI : 10.1126/science.286.5446.1921
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
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. ,
Phylogenetic position of guinea pigs revisited, Molecular Biology and Evolution, vol.14, issue.4, pp.461-464, 1997. ,
DOI : 10.1093/oxfordjournals.molbev.a025782
Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.233-257, 1967. ,
DOI : 10.2307/2406616
Nonparametric estimation of the number of classes in a population, Scand. J. Statis, vol.11, pp.265-270, 1984. ,
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
Random Variables and Probability Distributions, Cambrige Tracts in Mathematics, vol.36, 1937. ,
Summarizing a Posterior Distribution of Trees Using Agreement Subtrees, Systematic Biology, vol.56, issue.4, pp.578-590, 2007. ,
DOI : 10.1080/10635150701485091
On the estimation of the influence curve, Canadian Journal of Statistics, vol.18, issue.1, pp.1-9, 1995. ,
DOI : 10.2307/3315546
On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, 1859. ,
The guinea-pig is not a rodent, Nature, issue.6583, pp.381597-600, 1996. ,
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
Broad phylogenomic sampling improves resolution of the animal tree of life, Nature, vol.22, issue.7188, pp.452745-749, 2008. ,
DOI : 10.1038/nature06614
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
Neutral theory: The nulll hypothesis of molecular evolution, Nature Education, vol.1, issue.1, 2008. ,
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
Estimation of the branch points of a branching diffiasion process (with discussion), J. R. Stat. Soc. B, vol.32, pp.155-174, 1970. ,
The reconstruction of evolution, Annals of Human Genetics, vol.27, pp.105-106, 1963. ,
Phenetic and Phylogenetic Classification, chapter Reconstruction of evolutionary trees, Systematics Association Publ, issue.6, pp.67-76, 1964. ,
Bootstrap Methods: Another Look at the Jackknife, The Annals of Statistics, vol.7, issue.1, pp.1-26, 1979. ,
DOI : 10.1214/aos/1176344552
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
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
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
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
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
Advances in Cladistics, chapter The Logical Basis of Phylogenetic Analysis, pp.7-36, 1983. ,
Statistical Inference and the Estimation of Phylogenies, 1968. ,
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
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
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
Confidence Limits on Phylogenies: An Approach Using the Bootstrap, Evolution, vol.39, issue.4, pp.783-791, 1985. ,
DOI : 10.2307/2408678
Phylip (phylogeny inference package) version 3.6. Distributed by the author, 2005. ,
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
Statistical inference of phylogenies, J.R. Statist. Soc, vol.146, issue.3, pp.246-272, 1983. ,
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
Construction of Phylogenetic Trees, Science, vol.155, issue.3760, pp.279-284, 1967. ,
DOI : 10.1126/science.155.3760.279
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
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
Mathematics of evolution and phylogeny, 2005. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00185867
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
Experimental Design Criteria in Phylogenetics: Where to Add Taxa, Systematic Biology, vol.56, issue.4, pp.609-622, 2007. ,
DOI : 10.1080/10635150701499563
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
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
Statistical tests of models of DNA substitution, Journal of Molecular Evolution, vol.46, issue.2, pp.182-198, 1993. ,
DOI : 10.1007/BF00166252
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
Likelihood-Based Tests of Topologies in Phylogenetics, Systematic Biology, vol.49, issue.4, pp.652-670, 2000. ,
DOI : 10.1080/106351500750049752
Is the guinea-pig a rodent?, Nature, vol.351, issue.6328, pp.649-652, 1991. ,
DOI : 10.1038/351649a0
Fast and Reliable Reconstruction of Phylogenetic Trees with Very Short Edges, SODA: ACM-SIAM Symposium on Discrete Algorithms, pp.379-388, 2008. ,
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
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
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
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
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
Time Squared: Repeated Measures on Phylogenies, Molecular Biology and Evolution, vol.24, issue.2, pp.352-362, 2007. ,
DOI : 10.1093/molbev/msl165
Bootstrap and Edgeworth Expansion, 1984. ,
DOI : 10.1007/978-1-4612-4384-7
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
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
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
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
Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree, Mol Biol Evol, vol.11, pp.142-145, 1994. ,
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
Taxon sampling and the accuracy of phylogenetic analyses, J Mol Evol, vol.46, pp.239-257, 2008. ,
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
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
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
Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?, Systematic Biology, vol.52, issue.1, pp.124-126, 2003. ,
DOI : 10.1080/10635150390132911
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
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
Mathematics of evolution and phylogeny, chapter Statistical approach to tests involving phylogenies, pp.91-120, 2005. ,
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
Robust Statistics, 1981. ,
DOI : 10.1002/0471725250
Robust Statistics, 2004. ,
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
Handbook of Statistical Genetics, 3rd Edition, chapter Application of the Likelihood Function in Phylogenetic Analysis, pp.460-488, 2007. ,
Hypervariable ???minisatellite??? regions in human DNA, Nature, vol.12, issue.6006, pp.31467-73, 1985. ,
DOI : 10.1038/314067a0
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
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
Evolution of Protein Molecules, pp.21-132, 1969. ,
DOI : 10.1016/B978-1-4832-3211-9.50009-7
The advanced theory of statistics, 1973. ,
Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators, Systematic Biology, vol.47, issue.1, pp.43-60, 1998. ,
DOI : 10.1080/106351598261021
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
Evolutionary Rate at the Molecular Level, Nature, vol.16, issue.5129, pp.624-626, 1968. ,
DOI : 10.1038/217624a0
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
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
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
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol Biol Evol, vol.11, issue.3, pp.459-468, 1994. ,
On Information and Sufficiency, The Annals of Mathematical Statistics, vol.22, issue.1, pp.79-86, 1951. ,
DOI : 10.1214/aoms/1177729694
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
Theoretical comparisons of block bootstrap methods. The Annals of Statistics, pp.386-404, 1999. ,
Sequential changepoint detection in quality control and dynamical systems (with discussion), J. Roy. Statist. Soc. Ser. B, vol.57, pp.613-658, 1995. ,
Efficient recursive algorithms for detection of abrupt changes in signals and systems, IEEE Trans. Automatic Control, vol.44, pp.952-966, 1999. ,
A new method for calculating evolutionary substitution rates, Journal of Molecular Evolution, vol.46, issue.1, pp.86-93, 1984. ,
DOI : 10.1007/BF02101990
Detecting Internal Inconsistencies in Distance Data, Systematic Zoology, vol.34, issue.4, pp.397-403, 1985. ,
DOI : 10.2307/2413204
Evolution: The Remarkable History of a Scientific Theory. Modern Library, 2006. ,
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
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
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
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
Phylogenetic Tree Construction Using Markov Chain Monte Carlo, Journal of the American Statistical Association, vol.9, issue.450, 1996. ,
DOI : 10.1007/BF00161173
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
Estimating the number of classes. The Annals of Statistics, pp.917-930, 2007. ,
Concentration inequalities and model selection, 2006. ,
Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology, Systematic Biology, vol.56, issue.5, 2007. ,
DOI : 10.1080/10635150701627304
Mixed-up Trees: the Structure of Phylogenetic Mixtures, Bulletin of Mathematical Biology, vol.14, issue.2, 2007. ,
DOI : 10.1007/s11538-007-9293-y
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
A Quantitative Approach to a Problem in Classification, Evolution, vol.11, issue.2, pp.130-162, 1957. ,
DOI : 10.2307/2406046
The jackknife ? A review, Biometrika, vol.61, issue.1, pp.1-15, 1974. ,
Mathematics Of Evolution And Phylogeny, chapter How much can evolved characters tell us about the tree that generated them?, pp.384-312, 2005. ,
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
Statistical Methods in Molecular Evolution, Statistics for Biology and Health, 2004. ,
DOI : 10.1007/0-387-27733-1
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
A Multiple Testing Procedure for Clinical Trials, Biometrics, vol.35, issue.3, pp.549-556, 1979. ,
DOI : 10.2307/2530245
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
New Uses for New Phylogenies, chapter Inferring phylogenies from DNA sequence data: the effects of sampling, 1996. ,
CONTINUOUS INSPECTION SCHEMES, Biometrika, vol.41, issue.1-2, pp.100-114, 1954. ,
DOI : 10.1093/biomet/41.1-2.100
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
APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004. ,
DOI : 10.1093/bioinformatics/btg412
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
Reverend bayes on inference engines: A distributed hierarchical approach, AAAI-82 Proceedings, 1982. ,
Estimating the reliability of evolutionary trees, Molecular Biology and Evolution, vol.3, pp.403-417, 1986. ,
The Use of Tree Comparison Metrics, Systematic Zoology, vol.34, issue.1, pp.75-82, 1985. ,
DOI : 10.2307/2413347
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
Rodent monophyly: pitfalls of molecular phylogenies, J Mol Evol, vol.45, issue.6, pp.712-715, 1997. ,
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
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
Taxon sampling revisited, Nature, vol.383, issue.6725, pp.299-300, 1999. ,
DOI : 10.1038/18592
Increased Taxon Sampling Is Advantageous for Phylogenetic Inference, Systematic Biology, vol.51, issue.4, pp.664-671, 2002. ,
DOI : 10.1080/10635150290102357
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
MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998. ,
DOI : 10.1093/bioinformatics/14.9.817
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
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
Taxon Sampling and the Accuracy of Large Phylogenies, Systematic Biology, vol.47, issue.4, pp.702-710, 1998. ,
DOI : 10.1080/106351598260680
Lectures Note in mathematics, pp.119-126, 1979. ,
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
Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.425, issue.6960, pp.425798-804, 2003. ,
DOI : 10.1038/nature02053
MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1574, 2003. ,
DOI : 10.1093/bioinformatics/btg180
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
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
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
The Problem of Rooting Rapid Radiations, Molecular Biology and Evolution, vol.24, issue.11, pp.2400-2411, 2007. ,
DOI : 10.1093/molbev/msm178
An Approximately Unbiased Test of Phylogenetic Tree Selection, Systematic Biology, vol.51, issue.3, pp.492-508, 2002. ,
DOI : 10.1080/10635150290069913
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
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
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
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
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
Inverting Random Functions III: Discrete MLE Revisited, Annals of Combinatorics, vol.42, issue.3, 2006. ,
DOI : 10.1007/s00026-009-0023-z
On the variational distance of two trees, The Annals of Applied Probability, vol.16, issue.3, pp.1563-1575, 2006. ,
DOI : 10.1214/105051606000000196
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
The beta-blocker heart attack trial. beta-blocker heart attack study group, JAMA, vol.246, issue.18, pp.2073-2074, 1981. ,
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
Bootstrap Support Is Not First-Order Correct, Systematic Biology, vol.58, issue.2, 2009. ,
DOI : 10.1093/sysbio/syp016
PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.04beta, 2003. ,
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
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
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
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
Empirical Process Techniques for Dependent Data, chapter On Hoeffding's inequality for dependent random variables, pp.161-170, 2002. ,
Extensive Fungal Diversity in Plant Roots, Science, vol.295, issue.5562, p.2051, 2002. ,
DOI : 10.1126/science.295.5562.2051
MOLECULAR STRUCTURE OF NUCLEIC ACIDS, JAMA, vol.269, issue.15, pp.737-738, 1953. ,
DOI : 10.1001/jama.1993.03500150078030
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
Evolution and Topology in the Yeast Protein Interaction Network, Genome Research, vol.14, issue.7, pp.1310-1314, 2004. ,
DOI : 10.1101/gr.2300204
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. ,
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
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
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
Estimating the pattern of nucleotide substitution, Journal of Molecular Evolution, vol.39, issue.1, pp.105-111, 1994. ,
DOI : 10.1007/BF00178256
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
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
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
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