M. A. Harris, J. Clark, and A. Ireland, The Gene Ontology (GO) database and informatics resource, Nucleic Acids Res, vol.32, pp.258-61, 2009.

A. Levasseur and P. Pontarotti, The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics, Biol Direct, vol.6, p.11, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02645551

J. Huerta-cepas, S. Capella-gutierrez, and L. P. Pryszcz, PhylomeDB v3.0. an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions, Nucleic Acids Res, vol.39, pp.556-60, 2011.

S. Penel, A. M. Arigon, and J. F. Dufayard, Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.16, p.10, 2009.
URL : https://hal.archives-ouvertes.fr/lirmm-00400099

M. D. Lopez, T. Samuelsson, and . Egob, Gene Order Browser. Bioinformatics, vol.27, pp.1150-1151, 2011.

D. Wang, Y. Zhang, Z. Fan, G. Liu, and J. Yu, LGCbase: A comprehensive database for lineage-based co-regulated genes, Evol Bioinform Online, vol.8, pp.39-46, 2012.

L. Li, C. J. Stoeckert, R. D. Jr, and . Orthomcl, Identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, pp.2178-89, 2003.

B. Smith, W. Ceusters, and B. Klagges, Relations in biomedical ontologies, Genome Biol, vol.6, p.46, 2005.

P. Gouret, J. Paganini, and J. Dainat, Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: the multi-agent software system DAGOBAH, evolutionary biology-concepts, biodiversity, macroevolution and genome evolution, 2011.

P. Gouret, E. Danchin, A. Gilles, V. Vitiello, N. Balandraud et al., FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinformatics, vol.6, 0198.
URL : https://hal.archives-ouvertes.fr/hal-02681213

J. Paganini and P. Gouret, Reliable phylogenetic trees building: a new web interface for FIGENIX, Evolutionary Bioinformatics, 2012.

P. Gouret, J. D. Thompson, P. Pontarotti, and . Phylopattern, regular expressions to identify complex patterns in phylogenetic trees, BMC Bioinformatics, vol.10, p.298, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00663932

P. Flicek, B. L. Aken, and B. Ballester, Ensembl's 10th year, Nucleic Acids Research, vol.38, pp.557-62, 2010.

K. Katoh, K. Misawa, and K. Kuma, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, vol.30, pp.3059-66, 2002.

J. D. Thompson, V. Prigent, and O. Poch, LEON: multiple aLignment Evaluation Of Neighbours, Nucleic Acids Res, vol.32, pp.1298-307, 2004.

J. D. Thompson, A. Muller, and A. Waterhouse, MACSIMS: multiple alignment of complete sequences information management system, BMC Bioinformatics, vol.7, p.318, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00188166

M. Kanehisa and S. Goto, KEGG: kyoto encyclopaedia of genes and genomes, Nucleic Acids Res, vol.28, pp.27-30, 2000.

H. Parkinson, U. Sarkans, and N. Kolesnikov, ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments, Nucleic Acids Res, vol.39, pp.1002-1006, 2011.

D. Szklarczyk, A. Franceschini, and M. Kuhn, The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored, Nucleic Acids Res, vol.39, pp.561-569, 2011.

D. Binns, E. Dimmer, R. Huntley, D. Barrell, C. O'donovan et al., QuickGO: a web-based tool for Gene Ontology searching, Bioinformatics, vol.25, pp.3045-3051, 2009.

T. J. Hubbard, B. L. Aken, and S. Ayling, Nucleic Acids Res, vol.37, pp.690-697, 2009.

B. G. Mirkin, T. I. Fenner, M. Y. Galperin, and E. V. Koonin, Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes, BMC Evol Biol, vol.3, issue.2, 2003.

S. F. Altschul, T. L. Madden, and A. Schaffer, Gapped BLAST and PSI-BLAST-a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-402, 1997.

R. D. Finn, J. Mistry, and J. Tate, The Pfam protein families database, Nucleic Acids Res, vol.38, pp.211-233, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01294685

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

M. Long, E. Betran, K. Thornton, and W. Wang, The origin of new genes: glimpses from the young and old, Nat Rev Genet, vol.4, pp.865-75, 2003.

M. Nishikimi, R. Fukuyama, S. Minoshima, N. Shimizu, and K. Yagi, Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man, The Journal of biological chemistry, vol.269, pp.13685-13693, 1994.

Y. Ohta and M. Nishikimi, Random nucleotid substitution in primate nonfunctionnal gene for L-gulono-gammalactone oxidase, the missing enzyme L-ascorbic acid biosynthesis, Biochimica et Biophysica Acta (BBA), vol.1472, pp.408-4141, 1999.

A. Maeland and R. Waagbø, Examination of the qualitative ability of some cold water marine teleost to synthesis ascorbic acid, Comparative Biochemistry and Physiology, vol.121, pp.249-55, 1998.