E. Abouheif, R. Zardoya, and A. Meyer, Limitations of metazoan 18S rRNA sequence data: implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion, J. Mol. Evol, vol.47, pp.394-405, 1998.

A. Adoutte, G. Balavoine, N. Lartillot, and R. De-rosa, Animal evolution. The end of the intermediate taxa?, Trends Genet, vol.15, pp.104-108, 1999.

A. Adoutte, G. Balavoine, N. Lartillot, O. Lespinet, B. Prud'homme et al., The new animal phylogeny: reliability and implications, Proc. Natl Acad. Sci. USA, vol.97, pp.4453-4456, 2000.

A. M. Aguinaldo, J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey et al., , 1997.

, Evidence for a clade of nematodes, arthropods and other moulting animals, Nature, vol.387, pp.489-493

D. Arendt and K. Nubler-jung, Inversion of dorsoventral axis?, Nature, vol.371, 1994.

D. Baurain, H. Brinkmann, and H. Philippe, Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?, Mol. Biol. Evol, vol.24, pp.6-9, 2007.

J. E. Blair, K. Ikeo, T. Gojobori, and S. B. Hedges, The evolutionary position of nematodes, BMC Evol. Biol, vol.2, issue.7, 2002.

J. L. Boore, The use of genome-level characters for phylogenetic reconstruction, Trends Ecol. Evol, vol.21, pp.439-446, 2006.

S. J. Bourlat, Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida, Nature, vol.444, pp.85-88, 2006.

H. Brinkmann and H. Philippe, Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies, Mol. Biol. Evol, vol.16, pp.817-825, 1999.

R. C. Brusca and G. J. Brusca, , 1990.

C. Morris and S. , The fossil record and the early evolution of the Metazoa, Nature, vol.361, pp.219-225, 1993.

F. Delsuc, H. Brinkmann, and H. Philippe, Phylogenomics and the reconstruction of the tree of life, Nat. Rev. Genet, vol.6, pp.361-375, 2005.
URL : https://hal.archives-ouvertes.fr/halsde-00193293

F. Delsuc, H. Brinkmann, D. Chourrout, and H. Philippe, Tunicates and not cephalochordates are the closest living relatives of vertebrates, Nature, vol.439, pp.965-968, 2006.
URL : https://hal.archives-ouvertes.fr/halsde-00315436

H. Dopazo, J. Santoyo, and J. Dopazo, Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species, Bioinformatics, vol.20, pp.116-121, 2004.

J. Felsenstein, Cases in which parsimony or compatibility methods will be positively misleading, Syst. Zool, vol.27, pp.401-410, 1978.

J. Felsenstein, Inferring phylogenies, 2004.

K. G. Field, G. J. Olsen, D. J. Lane, S. J. Giovannoni, M. T. Ghiselin et al., Molecular phylogeny of the animal kingdom, Science, vol.239, pp.748-753, 1988.

P. G. Foster, Modeling compositional heterogeneity. Syst. Biol, vol.53, pp.485-495, 2004.

P. G. Foster and D. A. Hickey, Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions, J. Mol. Evol, vol.48, pp.284-290, 1999.
DOI : 10.1007/pl00006471

K. M. Halanych, The new view of animal phylogeny, Annu. Rev. Ecol. Evol. Syst, vol.35, pp.229-256, 2004.

K. M. Halanych, J. D. Bacheller, A. M. Aguinaldo, S. M. Liva, D. M. Hillis et al., Evidence from 18S ribosomal DNA that the lophophorates are protostome animals, Science, vol.267, pp.1641-1643, 1995.

M. D. Hendy and D. Penny, A framework for the quantitative study of evolutionary trees, Syst. Zool, vol.38, pp.297-309, 1989.

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

M. Irimia, I. Maeso, D. Penny, J. Garcia-fernandez, and S. W. Roy, Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata, Mol. Biol. Evol, vol.24, pp.1604-1607, 2007.

R. A. Jenner, Bilaterian phylogeny and uncritical recycling of morphological data sets, Syst. Biol, vol.50, pp.730-742, 2001.

G. Jobb, A. Von-haeseler, and K. Strimmer, TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics, BMC Evol. Biol, vol.4, 2004.

N. Lartillot and H. Philippe, A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process, Mol. Biol. Evol, vol.21, pp.1095-1109, 2004.
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 Evol. Biol, vol.7, 2007.
URL : https://hal.archives-ouvertes.fr/lirmm-00135024

D. V. Lavrov and B. F. Lang, Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements, Syst. Biol, vol.54, pp.651-659, 2005.

F. Marletaz, Chaetognath phylogenomics: a protostome with deuterostome-like development, Curr. Biol, vol.16, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00310882

D. Q. Matus, R. R. Copley, C. W. Dunn, A. Hejnol, H. Eccleston et al., Broad taxon and gene sampling indicate that chaetognaths are protostomes, Curr. Biol, vol.16, pp.575-576, 2006.

C. Nielsen, Animal evolution, interrelationships of the living phyla, 2001.

G. Olsen, Earliest phylogenetic branching: comparing rRNA-based evolutionary trees inferred with various techniques, Cold Spring Harb. Symp. Quant. Biol. LII, pp.825-837, 1987.

Y. Passamaneck and K. M. Halanych, Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly, Mol. Phylogenet. Evol, vol.40, pp.20-28, 2006.

K. J. Peterson and D. J. Eernisse, Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences, Evol. Dev, vol.3, pp.170-205, 2001.

H. Philippe and J. Laurent, How good are deep phylogenetic trees?, Curr. Opin. Genet. Dev, vol.8, pp.616-623, 1998.

H. Philippe and M. J. Telford, Large-scale sequencing and the new animal phylogeny, Trends Ecol. Evol, vol.21, pp.614-620, 2006.

H. Philippe, A. Chenuil, and A. Adoutte, Can the Cambrian explosion be inferred through molecular phylogeny?, Development, vol.120, pp.15-25, 1994.

H. Philippe, F. Delsuc, H. Brinkmann, and N. Lartillot, Phylogenomics. Annu. Rev. Ecol. Evol. Syst, vol.36, pp.541-562, 2005.

H. Philippe, N. Lartillot, and H. Brinkmann, Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia, Mol. Biol. Evol, vol.22, pp.1246-1253, 2005.
URL : https://hal.archives-ouvertes.fr/lirmm-00105354

H. Philippe, H. Brinkmann, P. Martinez, M. Riutort, `. et al., Acoel flatworms are not Platyhelminthes: evidence from phylogenomics, PLoS ONE, vol.2, 2007.

N. Rodriguez-ezpeleta, H. Brinkmann, B. Roure, N. Lartillot, B. F. Lang et al., Detecting and overcoming systematic errors in genome-scale phylogenies, 2007.

, Syst. Biol, vol.56, pp.389-399

I. B. Rogozin, Y. I. Wolf, L. Carmel, and E. V. Koonin, , 2007.

, Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements, Mol. Biol. Evol, vol.24, pp.1080-1090

A. Rokas, D. Kruger, and S. B. Carroll, Animal evolution and the molecular signature of radiations compressed in time, Science, vol.310, pp.1933-1938, 2005.

F. Ronquist and J. P. Huelsenbeck, Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.3, pp.1572-1574, 2003.

A. Stamatakis, T. Ludwig, and H. Meier, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, vol.21, pp.456-463, 2005.

M. J. Telford and G. E. Budd, The place of phylogeny and cladistics in evo-devo research, Int. J. Dev. Biol, vol.47, pp.479-490, 2003.

S. Whelan and N. Goldman, A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol. Biol. Evol, vol.18, pp.691-699, 2001.

Y. I. Wolf, I. B. Rogozin, and E. V. Koonin, Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis, Genome Res, vol.14, pp.29-36, 2004.

E. Zuckerkandl and L. Pauling, Molecules as documents of evolutionary history, J. Theor. Biol, vol.8, issue.65, pp.90083-90087, 1965.