T. Dobzhansky, Nothing in Biology Makes Sense Except in the Light of Evolution. The American Biology Teacher, pp.125-129, 1973.

A. Levasseur, L. Orlando, X. Bailly, M. Milinkovitch, E. Danchin et al., Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution, Biological Reviews, vol.162, issue.4, pp.551-72, 2007.
DOI : 10.1038/ng1812

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

P. Gouret, V. Vitiello, N. Balandraud, A. Gilles, P. Pontarotti et al., FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinformatics, vol.5, pp.6-198, 2005.

B. Engelhardt, M. Jordan, K. Muratore, S. Brenner, N. Krishnamurthy et al., Protein Molecular Function Prediction by Bayesian Phylogenomics, PLoS Computational Biology, vol.91, issue.5, pp.45-51, 2005.
DOI : 10.1371/journal.pcbi.0010045.sd001

C. Zmasek and S. Eddy, RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics, vol.16, pp.3-14, 2002.

O. Sakarya, K. Kosik, and T. Oakley, Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony, Bioinformatics, vol.24, issue.5, pp.606-618, 2008.
DOI : 10.1093/bioinformatics/btn005

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/24/5/606

D. Durand, B. Halldórsson, and B. Vernot, A Hybrid Micro???Macroevolutionary Approach to Gene Tree Reconstruction, Journal of Computational Biology, vol.13, issue.2, pp.320-355, 2006.
DOI : 10.1089/cmb.2006.13.320

R. Beiko and N. Hamilton, Phylogenetic identification of lateral genetic transfer events, BMC Evol Biol, vol.11, pp.6-15, 2006.

D. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-67, 2006.
DOI : 10.1093/molbev/msj030

T. Blomme, K. Vandepoele, D. Bodt, S. Simillion, C. Maere et al., The gain and loss of genes during 600 million years of vertebrate evolution, Genome Biology, vol.7, issue.5, p.43, 2006.
DOI : 10.1186/gb-2006-7-5-r43

L. Arvestad, A. Berglund, J. Lagergren, and B. Sennblad, Bayesian gene/species tree reconciliation and orthology analysis using MCMC, Bioinformatics, vol.19, issue.Suppl 1, pp.7-15, 2003.
DOI : 10.1093/bioinformatics/btg1000

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/19/suppl_1/i7

J. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-603, 2005.
DOI : 10.1093/bioinformatics/bti325

URL : https://hal.archives-ouvertes.fr/hal-00427861

D. Warren, L. Pereira, and F. Pereira, Prolog the language and its implementation compared with Lisp, Symposium on Artificial Intelligence and Programming Languages, 1977.

J. Mccarthy, Recursive Functions of Symbolic Expressions and Their Computation by Machine, Part I. Massachusetts Institute of Technology, 1960.

A. Wright and M. Fellensein, A Syntactic Approach to Type Soundness, Information and Computation, vol.115, issue.1, pp.38-94, 1992.
DOI : 10.1006/inco.1994.1093

J. Farris, Phylogenetic Analysis Under Dollo's Law, Systematic Zoology, vol.26, issue.1, pp.77-88, 1977.
DOI : 10.2307/2412867

URL : http://sysbio.oxfordjournals.org/cgi/content/short/26/1/77

J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.24, issue.6, pp.368-376, 1981.
DOI : 10.1007/BF01734359

J. Ruan, H. Li, Z. Chen, A. Coghlan, L. Coin et al., TreeFam: 2008 Update, Nucleic Acids Research, vol.36, issue.Database, pp.735-775, 2008.
DOI : 10.1093/nar/gkm1005

URL : http://doi.org/10.1093/nar/gkm1005

A. Bateman, E. Birney, R. Durbin, S. Eddy, K. Howe et al., The Pfam Protein Families Database, Nucleic Acids Research, vol.28, issue.1, pp.263-266, 2000.
DOI : 10.1093/nar/28.1.263

URL : https://hal.archives-ouvertes.fr/hal-01294685

T. Hubbard, B. Aken, S. Ayling, B. Ballester, K. Beal et al., 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

J. Thompson, A. Muller, A. Waterhouse, J. Procter, G. Barton et al., MACSIMS: multiple alignment of complete sequences information management system, BMC Bioinformatics, vol.23, pp.7-318, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00188166

C. Paulding, M. Ruvolo, and D. Haber, The Tre2 (USP6) oncogene is a hominoid-specific gene, Proceedings of the National Academy of Sciences, vol.100, issue.5, pp.2507-2511, 2003.
DOI : 10.1073/pnas.0437015100