M. Pellegrini, E. Marcotte, M. Thompson, D. Eisenberg, and T. Yeates, Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles, Proceedings of the National Academy of Sciences, vol.96, issue.8, pp.4285-4288, 1999.
DOI : 10.1073/pnas.96.8.4285
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16324

M. Huynen, B. Snel, W. Lathe, and P. Bork, Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences, Genome Research, vol.10, issue.8, pp.1204-1210
DOI : 10.1101/gr.10.8.1204
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310926

G. Glazko and A. Mushegian, Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns, Genome Biology, vol.5, issue.5, p.32, 2004.
DOI : 10.1186/gb-2004-5-5-r32

D. Liberles, A. Thoren, G. Von-heijne, and A. Elofsson, The Use of Phylogenetic Profiles for Gene Predictions, Current Genomics, vol.3, issue.3, pp.131-137, 2002.
DOI : 10.2174/1389202023350499

D. Barker and M. Pagel, Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes, PLoS Computational Biology, vol.17, issue.1, p.3, 2005.
DOI : 0022-2844(1981)017[0368:ETFDSA]2.0.CO;2

J. Vert, A tree kernel to analyse phylogenetic profiles, Bioinformatics, vol.18, issue.Suppl 1, pp.276-284, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S276
URL : https://hal.archives-ouvertes.fr/hal-00433591

S. Cokus, S. Mizutani, and M. Pellegrini, An improved method for identifying functionally linked proteins using phylogenetic profiles, BMC Bioinformatics, vol.8, issue.Suppl 4, p.7, 2002.
DOI : 10.1186/1471-2105-8-S4-S7
URL : http://doi.org/10.1186/1471-2105-8-s4-s7

P. Kensche, V. Van-noort, B. Dutilh, and M. Huynen, Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution, Journal of The Royal Society Interface, vol.359, issue.4, pp.151-170, 2008.
DOI : 10.1016/j.jmb.2006.04.011

E. Snitkin, A. Gustafson, J. Mellor, J. Wu, and C. Delisi, Comparative assessment of performance and genome dependence among phylogenetic profiling methods, BMC Bioinformatics, vol.7, issue.1, p.420, 2006.
DOI : 10.1186/1471-2105-7-420

R. Jothi, T. Przytycka, and L. Aravind, Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment, BMC Bioinformatics, vol.8, issue.1, p.173, 2007.
DOI : 10.1186/1471-2105-8-173

S. Singh and D. Wall, Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function, Evol Bioinf, vol.4, pp.217-223, 2008.

J. Ranea, C. Yeats, A. Grant, and C. Orengo, Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes, PLoS Computational Biology, vol.19, issue.11, p.237, 2008.
DOI : 10.1371/journal.pcbi.0030237.st004

O. Cordero, B. Snel, and P. Hogeweg, Coevolution of gene families in prokaryotes, Genome Research, vol.18, issue.3, pp.462-468, 2008.
DOI : 10.1101/gr.6815508

R. Tatusov, N. Fedorova, J. Jackson, A. Jacobs, B. Kiryutin et al., The COG database: an updated version includes eukaryotes, BMC Bioinformatics, vol.4, issue.1, p.41, 2008.
DOI : 10.1186/1471-2105-4-41

T. Tuller, M. Kupiec, and E. Ruppin, Co-evolutionary networks of genes and cellular processes across fungal species, Genome Biology, vol.10, issue.5, p.4, 2009.
DOI : 10.1186/gb-2009-10-5-r48

C. Von-mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork et al., STRING: a database of predicted functional associations between proteins, Nucleic Acids Research, vol.31, issue.1, pp.258-261, 2003.
DOI : 10.1093/nar/gkg034

F. Chen, A. Mackey, C. Stoeckert, and D. Roos, OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups, Nucleic Acids Research, vol.34, issue.90001, pp.363-368, 2006.
DOI : 10.1093/nar/gkj123

A. Altenhoff and C. Dessimoz, Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods, PLoS Computational Biology, vol.19, issue.1, p.1000262, 2009.
DOI : 10.1371/journal.pcbi.1000262.s018

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

S. Hunter, R. Apweiler, T. Attwood, A. Bairoch, A. Bateman et al., InterPro: the integrative protein signature database, C: InterPro: the integrative protein signature database, pp.211-215, 2009.
DOI : 10.1093/nar/gkn785
URL : https://hal.archives-ouvertes.fr/hal-01214141

K. Suhre, Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method, Methods Mol Biol, vol.396, pp.31-41, 2007.
DOI : 10.1385/1-59745-515-6:31

S. Baldauf, A. Roger, I. Wenk-siefert, and W. Doolittle, A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data, Science, vol.290, issue.5493, pp.972-977, 2000.
DOI : 10.1126/science.290.5493.972

E. Bapteste, H. Brinkmann, J. Lee, D. Moore, C. Sensen et al., The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba, Proceedings of the National Academy of Sciences, vol.99, issue.3, pp.1414-1419, 2002.
DOI : 10.1073/pnas.032662799

H. Philippe, N. Lartillot, and H. Brinkmann, Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia, Molecular Biology and Evolution, vol.22, issue.5, pp.1246-1253, 2005.
DOI : 10.1093/molbev/msi111
URL : https://hal.archives-ouvertes.fr/lirmm-00105354

N. Rodríguez-ezpeleta, H. Brinkmann, S. Burey, B. Roure, G. Burger et al., Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes, Current Biology, vol.15, issue.14, pp.1325-1330, 2005.
DOI : 10.1016/j.cub.2005.06.040

D. Moreira, . Heyden-s-von-der, D. Bass, P. López-garcía, E. Chao et al., Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata, Molecular Phylogenetics and Evolution, vol.44, issue.1, pp.255-266, 2007.
DOI : 10.1016/j.ympev.2006.11.001

A. Stechmann and T. Cavalier-smith, The root of the eukaryote tree pinpointed, Current Biology, vol.13, issue.17, pp.665-666, 2003.
DOI : 10.1016/S0960-9822(03)00602-X

J. Farris, Phylogenetic analysis under Dollo's Law. Syst Zoology, pp.77-88, 1977.
DOI : 10.1093/sysbio/26.1.77
URL : http://sysbio.oxfordjournals.org/cgi/content/short/26/1/77

E. Koonin, N. Fedorova, J. Jackson, A. Jacobs, D. Krylov et al., A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes, Genome Biology, vol.5, issue.2, p.7, 2004.
DOI : 10.1186/gb-2004-5-2-r7

D. Barker, A. Meade, and M. Pagel, Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes, Bioinformatics, vol.23, issue.1, pp.14-20, 2007.
DOI : 10.1093/bioinformatics/btl558

C. Martens, K. Vandepoele, and Y. De-peer, Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species, Proceedings of the National Academy of Sciences, vol.105, issue.9, pp.3427-3432, 2008.
DOI : 10.1073/pnas.0712248105

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005.
DOI : 10.1093/nar/gki198

C. Von-mering, L. Jensen, M. Kuhn, S. Chaffron, T. Doerks et al., STRING 7--recent developments in the integration and prediction of protein interactions, Nucleic Acids Research, vol.35, issue.Database, pp.358-362, 2007.
DOI : 10.1093/nar/gkl825

K. Aoki-kinoshita and M. Kanehisa, Gene Annotation and Pathway Mapping in KEGG, Methods Mol Biol, vol.396, pp.71-91, 2007.
DOI : 10.1007/978-1-59745-515-2_6

S. Date and E. Marcotte, Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages, Nature Biotechnology, vol.21, issue.9, pp.1055-1062, 2003.
DOI : 10.1038/nbt861