. Roussillon, Action Bioinformatique of the CNRS to EJPD. This is the contribution ISEM 2002-BBB of the Institut des Sciences de l, Evolution de Montpellier

A. , I. R. , and H. G. Morrison, Three retrotransposon families in the genome of Giardia lamblia: two telomeric, one dead, Proc. Natl. Acad. Sci. U S A, vol.98, pp.14497-502, 2001.

Y. Boucher, H. Huber, S. L. Haridon, K. O. Stetter, and W. F. Doolittle, Bacterial Origin for the Isoprenoid Biosynthesis Enzyme HMG-CoA Reductase of the Archaeal Orders Thermoplasmatales and Archaeoglobales, Molecular Biology and Evolution, vol.18, issue.7, pp.1378-88, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003922

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

T. R. Buckley and C. W. Cunningham, The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support, Molecular Biology and Evolution, vol.19, issue.4, pp.394-405, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004094

D. , C. J. , M. Dosay, M. S. Shivji, and M. J. Stanhope, In press. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks, Mol. Phylogenet. Evol, p.14

D. , E. J. , A. M. Pridgeon, P. Kores, H. P. Linder et al., Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences, Am. J. Bot, vol.86, pp.887-899, 1999.

E. , B. , E. Halloran, and S. Holmes, Bootstrap confidence levels for phylogenetic trees, Proc. Natl. Acad. Sci. U S A, vol.93, pp.13429-13434, 1996.

F. , J. , and H. Kishino, Is there something wrong with the bootstrap on phylogenies -a reply, Syst. Biol, vol.42, pp.193-200, 1993.

G. , N. , J. P. Anderson, and A. G. Rodrigo, Likelihood-based tests of topologies in phylogenetics, Syst. Biol, vol.49, pp.652-670, 2000.

H. , D. M. , and J. J. Bull, An empirical-test of bootstrapping as a method for assessing confidence in phylogenetic analysis, Syst. Biol, vol.42, pp.182-192, 1993.

H. , J. P. , and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, pp.754-755, 2001.

H. , J. P. , F. Ronquist, R. Nielsen, and J. P. Bollback, Bayesian inference of phylogeny and its impact on evolutionary biology, Science, vol.294, pp.2310-2314, 2001.

K. , K. G. , R. M. Mccourt, M. T. Cimino, and C. F. Delwiche, The closest living relatives of land plants, Science, vol.294, pp.2351-2354, 2001.

L. , B. , and D. L. Simon, Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees, Mol. Biol. Evol, vol.16, pp.750-759, 1999.

L. , A. D. , and T. W. Reeder, Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches, Syst. Biol, vol.51, pp.44-68, 2002.

L. , F. , M. Pagel, and V. R. , Major fungal lineages are derived from lichen symbiotic ancestors, Nature, vol.411, pp.937-977, 2001.

M. , C. M. , J. Czelusniak, M. P. Schneider, J. A. Muniz et al., Molecular phylogeny of ateline New World monkeys (Platyrrhini, Atelinae) based on gamma-globin gene sequences: evidence that Brachyteles is the sister group of Lagothrix, Mol. Phylogenet. Evol, vol.12, pp.10-30, 1999.

P. , D. , and K. A. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, pp.817-818, 1998.

R. , A. , and N. C. Grassly, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput, 1997.

S. , K. , A. Von, and . Haeseler, Quartet Puzzling: a quartet maximumlikelihood method for reconstructing tree topologies, Mol. Biol. Evol, vol.13, pp.964-969, 1996.

W. , P. J. , H. Kishino, and R. Ota, A Phylogenetic Foundation for Comparative Mammalian Genomics, Genome Informatics Series, vol.12, pp.141-155, 2001.

W. , L. A. , B. Slikas, D. W. Winkler, and F. H. Sheldon, Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences, Mol. Phylogenet. Evol, vol.22, pp.430-441, 2002.

W. , T. P. , D. J. Zwickl, T. A. Heath, and D. M. Hillis, In press. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support, Mol. Phylogenet. Evol