C. M. Thomas and K. M. Nielsen, Mechanisms of, and barriers to, horizontal gene transfer between bacteria, Nat Rev Microbiol, vol.3, pp.711-721, 2005.

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000.

J. P. Gogarten, W. F. Doolittle, and J. G. Lawrence, Prokaryotic evolution in light of gene transfer, Mol Biol Evol, vol.19, pp.2226-2238, 2002.

W. F. Doolittle, Phylogenetic classification and the universal tree, Science, vol.284, pp.2124-2129, 1999.

E. Bapteste, Do orthologous gene phylogenies really support treethinking?, BMC Evol Biol, vol.5, p.33, 2005.

E. Bapteste, Prokaryotic evolution and the tree of life are two different things, Biol Direct, vol.4, p.34, 2009.

T. Dagan and W. Martin, The tree of one percent, Genome Biol, vol.7, p.118, 2006.

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

J. N. Timmis, M. A. Ayliffe, C. Y. Huang, and W. Martin, Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes, Nat Rev Genet, vol.5, pp.123-135, 2004.

M. W. Gray, Origin and evolution of organelle genomes, Curr Opin Genet Dev, vol.3, pp.884-890, 1993.

J. Huang, Y. Xu, and J. P. Gogarten, The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic, Mol Biol Evol, vol.22, pp.2142-2146, 2005.

S. S. Abby, E. Tannier, M. Gouy, and V. Daubin, Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol.11, p.324, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00527151

D. Wu, A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea, Nature, vol.462, pp.1056-1060, 2009.

K. S. Pick, Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships, Mol Biol Evol, vol.27, pp.1983-1987, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00594637

H. Philippe, Phylogenomics revives traditional views on deep animal relationships, Curr Biol, vol.19, pp.706-712, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00594690

D. Moreira, L. Guyader, H. , and P. H. , Unusually high evolutionary rate of the elongation factor 1? genes from the Ciliophora and its impact on the phylogeny of eukaryotes, Mol Biol Evol, vol.16, pp.234-245, 1999.

M. Blum, The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance, Ann Appl Probab, vol.16, pp.2195-2214, 2006.

F. D. Ciccarelli, Toward automatic reconstruction of a highly resolved tree of life, Science, vol.311, pp.1283-1287, 2006.

K. P. Williams, Phylogeny of Gammaproteobacteria, J Bacteriol, vol.192, pp.2305-2314, 2010.

M. T. Alam, M. E. Merlo, E. Takano, and R. Breitling, Genome-based phylogenetic analysis of Streptomyces and its relatives, Mol Phylogenet Evol, vol.54, pp.763-772, 2010.

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

R. L. Tatusov, The COG database: An updated version includes eukaryotes, BMC Bioinformatics, vol.4, p.41, 2003.

R. L. Tatusov, E. V. Koonin, and D. J. Lipman, A genomic perspective on protein families, Science, vol.278, pp.631-637, 1997.

R. Jain, M. C. Rivera, and J. A. Lake, Horizontal gene transfer among genomes: The complexity hypothesis, Proc Natl Acad Sci, vol.96, pp.3801-3806, 1999.

Y. Nakamura, T. Itoh, H. Matsuda, and T. Gojobori, Biased biological functions of horizontally transferred genes in prokaryotic genomes, Nat Genet, vol.36, pp.760-766, 2004.

M. A. Ragan, On surrogate methods for detecting lateral gene transfer, FEMS Microbiol Lett, vol.201, issue.2, pp.187-191, 2001.

V. Daubin, N. A. Moran, and H. Ochman, Phylogenetics and the cohesion of bacterial genomes, Science, vol.301, pp.829-832, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00427390

B. Boussau, L. Guéguen, and M. Gouy, Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria, BMC Evol Biol, vol.8, p.272, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00428101

C. J. Creevey, T. Doerks, D. A. Fitzpatrick, J. Raes, and P. Bork, Universally distributed single-copy genes indicate a constant rate of horizontal transfer, PLoS ONE, vol.6, p.22099, 2011.

C. P. Andam and J. P. Gogarten, Biased gene transfer in microbial evolution, Nat Rev Microbiol, vol.9, pp.543-555, 2011.

C. P. Andam, D. Williams, and J. P. Gogarten, Biased gene transfer mimics patterns created through shared ancestry, Proc Natl Acad Sci, vol.107, pp.10679-10684, 2010.

B. Boussau and V. Daubin, Genomes as documents of evolutionary history, Trends Ecol Evol, vol.25, issue.4, pp.224-232, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00539397

S. Penel, Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.10, issue.6, p.3, 2009.
URL : https://hal.archives-ouvertes.fr/lirmm-00400099

E. W. Sayers, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.37, pp.5-15, 2009.

R. C. Edgar, MUSCLE: Multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol Biol Evol, vol.17, pp.540-552, 2000.

G. Jobb, V. Haeseler, A. Strimmer, and K. , TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics, BMC Evol Biol, vol.4, p.18, 2004.