R. Fleischmann, M. Adams, O. White, R. Clayton, and E. Kirkness, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, issue.5223, pp.496-512, 1995.
DOI : 10.1126/science.7542800

A. Enright, S. Van-dongen, and C. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575

G. Rubin, M. Yandell, J. Wortman, G. Miklos, G. Nelson et al., Comparative Genomics of the Eukaryotes, Science, vol.287, issue.5461, pp.2204-2215, 2000.
DOI : 10.1126/science.287.5461.2204

S. Henikoff, E. Greene, S. Pietrokovski, P. Bork, and T. Attwood, Gene Families: The Taxonomy of Protein Paralogs and Chimeras, Science, vol.278, issue.5338, pp.609-614, 1997.
DOI : 10.1126/science.278.5338.609

R. Tatusov, D. Natale, I. Garkavtsev, T. Tatusova, and U. Shankavaram, The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Research, vol.29, issue.1, pp.22-28, 2001.
DOI : 10.1093/nar/29.1.22

J. Gogarten and L. Olendzenski, Orthologs, paralogs and genome comparisons, Current Opinion in Genetics & Development, vol.9, issue.6, pp.630-636, 1999.
DOI : 10.1016/S0959-437X(99)00029-5

R. Tatusov, E. Koonin, and D. Lipman, A Genomic Perspective on Protein Families, Science, vol.278, issue.5338, pp.631-637, 1997.
DOI : 10.1126/science.278.5338.631

W. Fitch, Distinguishing Homologous from Analogous Proteins, Systematic Zoology, vol.19, issue.2, pp.99-113, 1970.
DOI : 10.2307/2412448

URL : http://sysbio.oxfordjournals.org/cgi/content/short/19/2/99

E. Sonnhammer and E. Koonin, Orthology, paralogy and proposed classification for paralog subtypes, Trends in Genetics, vol.18, issue.12, pp.619-620, 2002.
DOI : 10.1016/S0168-9525(02)02793-2

M. Huynen and P. Bork, Measuring genome evolution, Proceedings of the National Academy of Sciences, vol.95, issue.11, pp.5849-5856, 1998.
DOI : 10.1073/pnas.95.11.5849

M. Remm, C. Storm, and E. Sonnhammer, Automatic clustering of orthologs and in-paralogs from pairwise species comparisons, Journal of Molecular Biology, vol.314, issue.5, pp.1041-1052, 2001.
DOI : 10.1006/jmbi.2000.5197

L. Li, C. Stoeckert, J. Roos, and D. , OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003.
DOI : 10.1101/gr.1224503

T. Hulsen, M. Huynen, J. De-vlieg, and P. Groenen, Benchmarking ortholog identification methods using functional genomics data, Genome Biology, vol.7, issue.4, p.31, 2006.
DOI : 10.1186/gb-2006-7-4-r31

L. Jensen, P. Julien, M. Kuhn, C. Von-mering, and J. Muller, eggNOG: automated construction and annotation of orthologous groups of genes, Nucleic Acids Research, vol.36, issue.Database, pp.250-254, 2008.
DOI : 10.1093/nar/gkm796

E. Kriventseva, N. Rahman, O. Espinosa, and E. Zdobnov, OrthoDB: the hierarchical catalog of eukaryotic orthologs, Nucleic Acids Research, vol.36, issue.Database, pp.271-275, 2008.
DOI : 10.1093/nar/gkm845

T. Hubbard, B. Aken, S. Ayling, B. Ballester, and K. Beal, Ensembl 2009, Nucleic Acids Research, vol.37, issue.Database, pp.690-697, 2009.
DOI : 10.1093/nar/gkn828

URL : http://doi.org/10.1093/nar/gkn828

A. Schneider, C. Dessimoz, and G. Gonnet, OMA Browser Exploring orthologous relations across 352 complete genomes, Bioinformatics, vol.23, issue.16, pp.2180-2182, 2007.
DOI : 10.1093/bioinformatics/btm295

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/23/16/2180

E. Zdobnov, C. Von-mering, I. Letunic, and P. Bork, Consistency of genome-based methods in measuring Metazoan evolution, FEBS Letters, vol.32, issue.15, pp.3355-3361, 2005.
DOI : 10.1016/j.febslet.2005.04.006

E. Zdobnov and P. Bork, Quantification of insect genome divergence, Trends in Genetics, vol.23, issue.1, pp.16-20, 2007.
DOI : 10.1016/j.tig.2006.10.004

C. Creevey, T. Doerks, D. Fitzpatrick, J. Raes, and P. Bork, Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer, PLoS ONE, vol.23, issue.8, p.22099, 2011.
DOI : 10.1371/journal.pone.0022099.s009

K. Wolfe and D. Shields, Molecular evidence for an ancient duplication of the entire yeast genome, Nature, vol.387, issue.6634, pp.708-713, 1997.
DOI : 10.1038/42711

E. Koonin, A. Mushegian, and P. Bork, Non-orthologous gene displacement, Trends in Genetics, vol.12, issue.9, pp.334-336, 1996.
DOI : 10.1016/0168-9525(96)20010-1

F. Ciccarelli, T. Doerks, C. Von-mering, C. Creevey, and B. Snel, Toward Automatic Reconstruction of a Highly Resolved Tree of Life, Science, vol.311, issue.5765, pp.1283-1287, 2006.
DOI : 10.1126/science.1123061

C. Creevey, D. Fitzpatrick, G. Philip, R. Kinsella, O. Connell et al., Does a tree-like phylogeny only exist at the tips in the prokaryotes?, Proceedings of the Royal Society B: Biological Sciences, vol.271, issue.1557, pp.2551-2558, 2004.
DOI : 10.1098/rspb.2004.2864

A. Rokas, B. Williams, N. King, and S. Carroll, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.425, issue.6960, pp.798-804, 2003.
DOI : 10.1038/nature02053

C. Dunn, A. Hejnol, D. Matus, K. Pang, and W. Browne, Broad phylogenomic sampling improves resolution of the animal tree of life, Nature, vol.22, issue.7188, pp.745-749, 2008.
DOI : 10.1038/nature06614

G. Parra, K. Bradnam, and I. Korf, CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, vol.23, issue.9, pp.1061-1067, 2007.
DOI : 10.1093/bioinformatics/btm071

J. Mondego, M. Carazzolle, G. Costa, E. Formighieri, and L. Parizzi, A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao, BMC Genomics, vol.9, issue.1, p.548, 2008.
DOI : 10.1186/1471-2164-9-548

S. Diguistini, N. Liao, D. Platt, G. Robertson, and M. Seidel, De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data, Genome Biology, vol.10, issue.9, p.94, 2009.
DOI : 10.1186/gb-2009-10-9-r94

S. Richards, R. Gibbs, G. Weinstock, S. Brown, and R. Denell, The genome of the model beetle and pest Tribolium castaneum, Nature, vol.107, issue.7190, pp.949-955, 2008.
DOI : 10.1038/nature06784

M. Hubisz, M. Lin, M. Kellis, and A. Siepel, Error and Error Mitigation in Low-Coverage Genome Assemblies, PLoS ONE, vol.14, issue.2, p.17034, 2011.
DOI : 10.1371/journal.pone.0017034.s015

B. Linard, J. Thompson, O. Poch, and O. Lecompte, OrthoInspector: comprehensive orthology analysis and visual exploration, BMC Bioinformatics, vol.12, issue.1, p.11, 2011.
DOI : 10.1186/1471-2105-12-11

URL : https://hal.archives-ouvertes.fr/inserm-00663697

K. Trachana, T. Larsson, S. Powell, W. Chen, and T. Doerks, Orthology prediction methods: A quality assessment using curated protein families, BioEssays, vol.59, issue.10, pp.769-80, 2011.
DOI : 10.1002/bies.201100062

R. Page and M. Charleston, Reconciled trees and incongruent gene and species trees In: Dimacs series in discrete mathematics and theoretical computer science, pp.57-70, 1997.

R. Sorek, Y. Zhu, C. Creevey, M. Francino, and P. Bork, Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer, Science, vol.318, issue.5855, pp.1449-1452, 2007.
DOI : 10.1126/science.1147112

R. Page and M. Charleston, From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem, Molecular Phylogenetics and Evolution, vol.7, issue.2, pp.231-240, 1997.
DOI : 10.1006/mpev.1996.0390

M. Telford and R. Copley, Animal Phylogeny: Fatal Attraction, Current Biology, vol.15, issue.8, pp.296-299, 2005.
DOI : 10.1016/j.cub.2005.04.001

URL : http://doi.org/10.1016/j.cub.2005.04.001

S. Altschul, T. Madden, A. Schaffer, J. Zhang, and Z. Zhang, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

D. Knowles and A. Mclysaght, Recent de novo origin of human protein-coding genes, Genome Research, vol.19, issue.10, pp.1752-1759, 2009.
DOI : 10.1101/gr.095026.109

P. Dehal, Y. Satou, R. Campbell, J. Chapman, and B. Degnan, The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins, Science, vol.298, issue.5601, pp.2157-2167, 2002.
DOI : 10.1126/science.1080049

URL : https://hal.archives-ouvertes.fr/hal-00311352

A. Hejnol, M. Obst, A. Stamatakis, M. Ott, and G. Rouse, Assessing the root of bilaterian animals with scalable phylogenomic methods, Proceedings of the Royal Society B: Biological Sciences, vol.1, issue.3, pp.4261-4270, 2009.
DOI : 10.1006/jtbi.1999.0999

G. Fang, N. Bhardwaj, R. Robilotto, and M. Gerstein, Getting Started in Gene Orthology and Functional Analysis, PLoS Computational Biology, vol.96, issue.1858, p.1000703
DOI : 10.1371/journal.pcbi.1000703.s001

M. Milinkovitch, R. Helaers, E. Depiereux, A. Tzika, and T. Gabaldon, 2?? genomes - depth does matter, Genome Biology, vol.11, issue.2, p.16
DOI : 10.1186/gb-2010-11-2-r16

URL : http://doi.org/10.1186/gb-2010-11-2-r16

A. Vilella, E. Birney, P. Flicek, and J. Herrero, Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses, Genome Biology, vol.12, issue.2, p.401, 2011.
DOI : 10.1186/gb-2011-12-2-401

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

URL : http://doi.org/10.1093/nar/gkh340

G. Talavera and J. Castresana, Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments, Systematic Biology, vol.56, issue.4, pp.564-577, 2007.
DOI : 10.1080/10635150701472164

J. Felsenstein, Phylip -phylogeny inference package (version 3.2), Cladistics, vol.5, pp.164-166, 1989.

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

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, issue.1, pp.127-128, 2007.
DOI : 10.1093/bioinformatics/btl529

F. Ciccarelli, C. Von-mering, M. Suyama, E. Harrington, and E. Izaurralde, Complex genomic rearrangements lead to novel primate gene function, Genome Research, vol.15, issue.3, pp.343-351, 2005.
DOI : 10.1101/gr.3266405

J. Muller, C. Creevey, J. Thompson, D. Arendt, and P. Bork, AQUA: automated quality improvement for multiple sequence alignments, Bioinformatics, vol.26, issue.2, pp.263-265, 2010.
DOI : 10.1093/bioinformatics/btp651

J. Thompson, J. Thierry, and O. Poch, RASCAL: rapid scanning and correction of multiple sequence alignments, Bioinformatics, vol.19, issue.9, pp.1155-1161, 2003.
DOI : 10.1093/bioinformatics/btg133

C. Creevey and J. Mcinerney, Clann: investigating phylogenetic information through supertree analyses, Bioinformatics, vol.21, issue.3, pp.390-392, 2005.
DOI : 10.1093/bioinformatics/bti020

URL : http://cadair.aber.ac.uk/dspace/bitstream/2160/12868/1/Creevey_2005_Clann_Construction_of_Supertrees_and_exploration_of_phylogenomic_information_from_partially_overlapping_datasets.pdf

D. Gilbert, Sequence File Format Conversion with Command-Line Readseq, Curr Protoc Bioinformatics Appendix, vol.1, p.1, 2003.
DOI : 10.1002/0471250953.bia01es00

C. Wu, C. Orozco, J. Boyer, M. Leglise, and J. Goodale, BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources, Genome Biology, vol.10, issue.11, p.130, 2009.
DOI : 10.1186/gb-2009-10-11-r130

J. Muller, Y. Oma, L. Vallar, E. Friederich, and O. Poch, Sequence and Comparative Genomic Analysis of Actin-related Proteins, Molecular Biology of the Cell, vol.16, issue.12, pp.5736-5748, 2005.
DOI : 10.1091/mbc.E05-06-0508

URL : https://hal.archives-ouvertes.fr/hal-00187704

P. Saebo, S. Andersen, J. Myrseth, J. Laerdahl, and T. Rognes, PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology, Nucleic Acids Research, vol.33, issue.Web Server, pp.535-539, 2005.
DOI : 10.1093/nar/gki423

URL : http://doi.org/10.1093/nar/gki423

K. Pruitt, T. Tatusova, and D. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Research, vol.35, issue.Database, pp.61-65, 2007.
DOI : 10.1093/nar/gkl842

S. Eddy, Hidden Markov models, Current Opinion in Structural Biology, vol.6, issue.3, pp.361-365, 1996.
DOI : 10.1016/S0959-440X(96)80056-X

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

D. Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods) Version 4: Sinauer Associates, 2002.