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

R. Jain, M. Rivera, and J. Lake, Horizontal gene transfer among genomes: The complexity hypothesis, Proceedings of the National Academy of Sciences, vol.96, issue.7, pp.3801-3806, 1999.
DOI : 10.1073/pnas.96.7.3801

I. Choi and S. Kim, Global extent of horizontal gene transfer, Proceedings of the National Academy of Sciences, vol.104, issue.11, pp.4489-4494, 2007.
DOI : 10.1073/pnas.0611557104

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

M. Lynch and J. Conery, The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, issue.5494, pp.1151-1155, 2000.
DOI : 10.1126/science.290.5494.1151

M. Hahn, M. Han, and S. Han, Gene Family Evolution across 12 Drosophila Genomes, PLoS Genetics, vol.20, issue.11, p.197, 2007.
DOI : 10.1371/journal.pgen.0030197.st004

URL : http://doi.org/10.1371/journal.pgen.0030197

W. Doolittle, Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2129, 1999.
DOI : 10.1126/science.284.5423.2124

N. Galtier and V. Daubin, Dealing with incongruence in phylogenomic analyses, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.449, issue.7158, pp.4023-4029, 2008.
DOI : 10.1038/nature06107

URL : https://hal.archives-ouvertes.fr/hal-00428227

C. House, The Tree of Life Viewed Through the Contents of Genomes, Methods Mol Biol, vol.532, pp.141-161, 2009.
DOI : 10.1007/978-1-60327-853-9_8

M. Rivera and J. Lake, The ring of life provides evidence for a genome fusion origin of eukaryotes, Nature, vol.87, issue.7005, pp.152-155, 2004.
DOI : 10.1093/nar/25.17.3389

J. Eisen and C. Fraser, Phylogenomics: Intersection of Evolution and Genomics, Science, vol.300, issue.5626, pp.1706-1707, 2003.
DOI : 10.1126/science.1086292

F. Tekaia, A. Lazcano, and B. Dujon, The genomic tree as revealed from whole proteome comparisons, Genome Res, vol.9, issue.6, pp.550-557, 1999.

F. Tekaia and E. Yeramian, Genome Trees from Conservation Profiles, PLoS Computational Biology, vol.93, issue.7, p.75, 2005.
DOI : 10.1371/journal.pcbi.0010075.st001

M. Lynch and J. Conery, The evolutionary demography of duplicate genes, J Struct Funct Genomics, vol.3, pp.35-44, 2003.
DOI : 10.1007/978-94-010-0263-9_4

E. Koonin, Orthologs, Paralogs, and Evolutionary Genomics, Annual Review of Genetics, vol.39, issue.1, pp.309-338, 2005.
DOI : 10.1146/annurev.genet.39.073003.114725

A. Kuzniar, R. Van-ham, S. Pongor, and J. Leunissen, The quest for orthologs: finding the corresponding gene across genomes, Trends in Genetics, vol.24, issue.11, pp.539-551, 2008.
DOI : 10.1016/j.tig.2008.08.009

M. Novo, F. Bigey, and E. Beyne, Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118, Proceedings of the National Academy of Sciences, vol.106, issue.38, pp.16333-16338, 2009.
DOI : 10.1073/pnas.0904673106

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

D. Kristensen, L. Kannan, and M. Coleman, A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches, Bioinformatics, vol.26, issue.12, pp.1481-1487, 2010.
DOI : 10.1093/bioinformatics/btq229

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

W. Fitch, Homology, Trends in Genetics, vol.16, issue.5, pp.227-231, 2000.
DOI : 10.1016/S0168-9525(00)02005-9

F. Tekaia and B. Dujon, Pervasiveness of Gene Conservation and Persistence of Duplicates in Cellular Genomes, Journal of Molecular Evolution, vol.49, issue.5, pp.591-600, 1999.
DOI : 10.1007/PL00006580

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

K. Wolfe, Robustness???it's not where you think it is, Nature Genetics, vol.71, issue.1, pp.3-4, 2000.
DOI : 10.1038/75560

S. Ohno, Evolution by Gene Duplication, 1970.
DOI : 10.1007/978-3-642-86659-3

V. Babenko and D. Krylov, Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved, Nucleic Acids Research, vol.32, issue.17, pp.5029-5035, 2004.
DOI : 10.1093/nar/gkh833

A. Nasir, K. Kim, and G. Caetano-anollés, Global Patterns of Protein Domain Gain and Loss in Superkingdoms, PLoS Computational Biology, vol.431, issue.16, p.1003452, 2014.
DOI : 10.1371/journal.pcbi.1003452.s004

A. Moore and E. Bornberg-bauer, The Dynamics and Evolutionary Potential of Domain Loss and Emergence, Molecular Biology and Evolution, vol.29, issue.2, pp.787-796, 2012.
DOI : 10.1093/molbev/msr250

A. Geneva, C. Muirhead, S. Kingan, and D. Garrigan, A New Method to Scan Genomes for Introgression in a Secondary Contact Model, PLOS ONE, vol.188, issue.4, p.118621, 2015.
DOI : 10.1371/journal.pone.0118621.s015

Y. Nakatani, H. Takeda, Y. Kohara, and S. Morishita, Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

D. Dalquen, A. Altenhoff, G. Gonnet, and C. Dessimoz, The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study, PLoS ONE, vol.11, issue.2, 2013.
DOI : 10.1371/journal.pone.0056925.s002

P. Worning, L. Jensen, K. Nelson, S. Brunak, and D. Ussery, Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima, Nucleic Acids Research, vol.28, issue.3, pp.706-709, 2000.
DOI : 10.1093/nar/28.3.706

T. Dagan, Y. Artzy-randrup, and W. Martin, Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution, Proceedings of the National Academy of Sciences, vol.105, issue.29, pp.10039-10044, 2008.
DOI : 10.1073/pnas.0800679105

D. Fitzpatrick, Horizontal gene transfer in fungi, FEMS Microbiology Letters, vol.329, issue.1, pp.1-8, 2012.
DOI : 10.1111/j.1574-6968.2011.02465.x

A. Crisp, C. Boschetti, M. Perry, A. Tunnacliffe, and G. Micklem, Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes, Genome Biology, vol.16, issue.1, p.50, 2015.
DOI : 10.1038/75556

V. Galeote, F. Bigey, and E. Beyne, Amplification of a Zygosaccharomyces bailii DNA Segment in Wine Yeast Genomes by Extrachromosomal Circular DNA Formation, PLoS ONE, vol.24, issue.3, p.17872, 2011.
DOI : 10.1371/journal.pone.0017872.s002

URL : https://hal.archives-ouvertes.fr/hal-01222409

K. Liu, E. Steinberg, A. Yozzo, Y. Song, M. Kohn et al., Interspecific introgressive origin of genomic diversity in the house mouse, Proceedings of the National Academy of Sciences, vol.112, issue.1, pp.196-201, 2015.
DOI : 10.1073/pnas.1406298111

M. Ravenhall, N. ?kunca, F. Lassalle, and C. Dessimoz, Inferring Horizontal Gene Transfer, PLOS Computational Biology, vol.1079, issue.1, p.1004095, 2015.
DOI : 10.1371/journal.pcbi.1004095.s002

URL : http://doi.org/10.1371/journal.pcbi.1004095

M. Syvanen, Evolutionary Implications of Horizontal Gene Transfer, Annual Review of Genetics, vol.46, issue.1, pp.341-358, 2012.
DOI : 10.1146/annurev-genet-110711-155529

K. Forslund and E. Sonnhammer, Evolution of Protein Domain Architectures, Methods Mol Biol, vol.856, pp.187-216, 2012.
DOI : 10.1007/978-1-61779-585-5_8

J. Weiner, . Iii, F. Beaussart, and E. Bornberg-bauer, Domain deletions and substitutions in the modular protein evolution, FEBS Journal, vol.30, issue.Suppl. 1, pp.2037-2047, 2006.
DOI : 10.1111/j.1742-4658.2006.05220.x

E. Bornberg-bauer, A. Huylmans, and T. Sikosek, How do new proteins arise?, Current Opinion in Structural Biology, vol.20, issue.3, pp.390-396, 2010.
DOI : 10.1016/j.sbi.2010.02.005

M. Levitt, Nature of the protein universe, Proceedings of the National Academy of Sciences, vol.106, issue.27, pp.11079-11084, 2009.
DOI : 10.1073/pnas.0905029106

N. Song, J. Joseph, G. Davis, and D. Durand, Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins, PLoS Computational Biology, vol.20, issue.5, p.1000063, 2008.
DOI : 10.1371/journal.pcbi.1000063.s008

M. Omelchenko, M. Galperin, Y. Wolf, and E. Koonin, Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution, Biology Direct, vol.5, issue.1, p.31, 2010.
DOI : 10.1186/1745-6150-5-31

J. Capra, K. Pollard, and M. Singh, Novel genes exhibit distinct patterns of function acquisition and network integration, Genome Biology, vol.11, issue.12, p.127, 2010.
DOI : 10.1186/gb-2010-11-12-r127

M. Long, E. Betran, K. Thornton, and W. Wang, The origin of new genes: glimpses from the young and old, Nature Reviews Genetics, vol.4, issue.11, pp.865-875, 2003.
DOI : 10.1038/nrg1204

M. Giacomelli, A. Hancock, and J. Masel, The Conversion of 3' UTRs into Coding Regions, Molecular Biology and Evolution, vol.24, issue.2, pp.457-464, 2007.
DOI : 10.1093/molbev/msl172

D. Kristensen, Y. Wolf, A. Mushegian, and E. Koonin, Computational methods for Gene Orthology inference, Briefings in Bioinformatics, vol.12, issue.5, pp.379-391, 2011.
DOI : 10.1093/bib/bbr030

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

F. Chen, A. Mackey, J. Vermunt, and D. Roos, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, PLoS ONE, vol.17, issue.4, p.383, 2007.
DOI : 10.1371/journal.pone.0000383.s008

K. Trachana, T. Larsson, and S. Powell, Orthology prediction methods: A quality assessment using curated protein families, BioEssays, vol.59, issue.10, pp.769-780, 2011.
DOI : 10.1002/bies.201100062

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

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, . Jr, 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

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

L. Jensen, P. Julien, and M. Kuhn, 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

A. Ivliev and M. Sergeeva, ORTHOFOCUS: PROGRAM FOR IDENTIFICATION OF ORTHOLOGS IN MULTIPLE GENOMES IN FAMILY-FOCUSED STUDIES, Journal of Bioinformatics and Computational Biology, vol.06, issue.04, pp.811-824, 2008.
DOI : 10.1142/S0219720008003692

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

F. Tekaia and E. Yeramian, SuperPartitions: Detection and classification of orthologs, Gene, vol.492, issue.1, pp.199-211, 2012.
DOI : 10.1016/j.gene.2011.10.027

URL : https://hal.archives-ouvertes.fr/pasteur-00647177

D. Emms and S. Kelly, OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biology, vol.24, issue.1, p.157, 2015.
DOI : 10.1186/s13059-015-0721-2

T. Deluca, I. Wu, and J. Pu, Roundup: a multi-genome repository of orthologs and evolutionary distances, Bioinformatics, vol.22, issue.16, pp.2044-2046, 2006.
DOI : 10.1093/bioinformatics/btl286

D. Wall and T. Deluca, Ortholog Detection Using the Reciprocal Smallest Distance Algorithm, Methods Mol Biol, vol.396, pp.95-110, 2007.
DOI : 10.1007/978-1-59745-515-2_7

A. Roth, G. Gonnet, and C. Dessimoz, Algorithm of OMA for large-scale orthology inference, BMC Bioinformatics, vol.9, issue.1, p.518, 2008.
DOI : 10.1186/1471-2105-9-518

K. Kim, S. Sung, G. Caetano-anollés, J. Han, and H. Kim, An approach of orthology detection from homologous sequences under minimum evolution, Nucleic Acids Research, vol.36, issue.17, p.110, 2008.
DOI : 10.1093/nar/gkn485

G. Shi, L. Zhang, and T. Jiang, MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement, BMC Bioinformatics, vol.11, issue.1, p.10, 2010.
DOI : 10.1186/1471-2105-11-10

L. Salichos and A. Rokas, Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade, PLoS ONE, vol.449, issue.4, p.18755, 2011.
DOI : 10.1371/journal.pone.0018755.s002

C. Storm and E. Sonnhammer, Automated ortholog inference from phylogenetic trees and calculation of orthology reliability, Bioinformatics, vol.18, issue.1, pp.92-99, 2002.
DOI : 10.1093/bioinformatics/18.1.92

C. Zmasek and S. Eddy, RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics, vol.3, issue.1, p.14, 2004.
DOI : 10.1186/1471-2105-3-14

P. Dehal and J. Boore, A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database, BMC Bioinformatics, vol.7, issue.1, p.201, 2006.
DOI : 10.1186/1471-2105-7-201

L. Goodstadt and C. Ponting, Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human, PLoS Computational Biology, vol.49, issue.9, p.133, 2006.
DOI : 1434-5161(2004)049[0548:ADTPAI]2.0.CO;2

H. Li, A. Coghlan, and J. Ruan, TreeFam: a curated database of phylogenetic trees of animal gene families, Nucleic Acids Research, vol.34, issue.90001, pp.572-580, 2006.
DOI : 10.1093/nar/gkj118

R. Van-der-heijden, B. Snel, V. Van-noort, and M. Huynen, Orthology prediction at scalable resolution by phylogenetic tree analysis, BMC Bioinformatics, vol.8, issue.1, p.83, 2007.
DOI : 10.1186/1471-2105-8-83

A. Vilella, J. Severin, A. Ureta-vidal, L. Heng, R. Durbin et al., EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates, Genome Research, vol.19, issue.2, pp.327-335, 2009.
DOI : 10.1101/gr.073585.107

I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, Automatic genome-wide reconstruction of phylogenetic gene trees, Bioinformatics, vol.23, issue.13, pp.549-558, 2007.
DOI : 10.1093/bioinformatics/btm193

R. Datta, C. Meacham, and B. Samad, Berkeley PHOG: PhyloFacts orthology group prediction web server, Nucleic Acids Research, vol.37, issue.Web Server, pp.84-89, 2009.
DOI : 10.1093/nar/gkp373

R. Jothi, E. Zotenko, A. Tasneem, and T. Przytycka, COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations, Bioinformatics, vol.22, issue.7, pp.779-788, 2006.
DOI : 10.1093/bioinformatics/btl009

T. Gabaldón, Large-scale assignment of orthology: back to phylogenetics?, Genome Biology, vol.9, issue.10, p.235, 2008.
DOI : 10.1186/gb-2008-9-10-235

J. Thompson, B. Linard, O. Lecompte, and O. Poch, A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives, PLoS ONE, vol.15, issue.31, p.18093, 2011.
DOI : 10.1371/journal.pone.0018093.t001

M. Poptsova and J. Gogarten, BranchClust: a phylogenetic algorithm for selecting gene families, BMC Bioinformatics, vol.8, issue.1, p.120, 2007.
DOI : 10.1186/1471-2105-8-120

C. Dessimoz and M. Gil, Phylogenetic assessment of alignments reveals neglected tree signal in gaps, Genome Biology, vol.11, issue.4, p.37, 2010.
DOI : 10.1186/gb-2010-11-4-r37

E. Bapteste, Y. Boucher, J. Leigh, and W. Doolittle, Phylogenetic reconstruction and lateral gene transfer, Trends in Microbiology, vol.12, issue.9, pp.406-411, 2004.
DOI : 10.1016/j.tim.2004.07.002

S. Cannon and N. Young, OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies, BMC Bioinformatics, vol.4, issue.1, p.35, 2003.
DOI : 10.1186/1471-2105-4-35

I. Wapinski and A. Regev, Reconstructing Gene Histories in Ascomycota Fungi, Methods Enzymol, vol.470, pp.447-485, 2010.
DOI : 10.1016/S0076-6879(10)70018-5

E. Passarge, B. Horsthemke, and R. Farber, Incorrect use of the term synteny, Nature Genetics, vol.23, issue.4, p.387, 1999.
DOI : 10.1038/70486

G. Fischer, S. James, I. Roberts, S. Oliver, and E. Louis, Chromosomal evolution in Saccharomyces, Nature, vol.405, pp.451-454, 2000.

F. Lemoine, O. Lespinet, and B. Labedan, Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data, BMC Evolutionary Biology, vol.7, issue.1, p.237, 2007.
DOI : 10.1186/1471-2148-7-237

URL : https://hal.archives-ouvertes.fr/hal-00194466

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

J. Souciet, B. Dujon, and C. Gaillardin, Comparative genomics of protoploid Saccharomycetaceae, Genome Res, vol.19, pp.1696-1709, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00407511

X. Zheng, F. Lu, Z. Wang, F. Zhong, J. Hoover et al., Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs, Bioinformatics, vol.21, issue.6, pp.703-710, 2005.
DOI : 10.1093/bioinformatics/bti045

J. Catchen, J. Conery, and J. Postlethwait, Automated identification of conserved synteny after whole-genome duplication, Genome Research, vol.19, issue.8, pp.1497-1505, 2009.
DOI : 10.1101/gr.090480.108

K. Byrne and K. Wolfe, Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser, Nucleic Acids Research, vol.34, issue.90001, pp.452-455, 2006.
DOI : 10.1093/nar/gkj041

M. Seret, J. Diffels, A. Goffeau, and P. Baret, Combined phylogeny and neighborhood analysis of the evolution of the ABC transporters conferring multiple drug resistance in hemiascomycete yeasts, BMC Genomics, vol.10, issue.1, p.459, 2009.
DOI : 10.1186/1471-2164-10-459

M. Kellis, N. Patterson, B. Birren, B. Berger, and E. Lander, Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery, Journal of Computational Biology, vol.11, issue.2-3, pp.319-355, 2004.
DOI : 10.1089/1066527041410319

K. Byrne and K. Wolfe, The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species, Genome Research, vol.15, issue.10, pp.1456-1461, 2005.
DOI : 10.1101/gr.3672305

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, 2010.
DOI : 10.1371/journal.pcbi.1000703.s001

N. Yosef, R. Sharan, and W. Noble, Improved network-based identification of protein orthologs, Bioinformatics, vol.24, issue.16, pp.200-206, 2008.
DOI : 10.1093/bioinformatics/btn277

F. Towfic, S. Vanderplas, and C. Oliver, Detection of gene orthology from gene co-expression and protein interaction networks, BMC Bioinformatics, vol.11, issue.Suppl 3, p.7, 2010.
DOI : 10.1186/1471-2105-11-S3-S7

D. Park, R. Singh, M. Baym, C. Liao, and B. Berger, IsoBase: a database of functionally related proteins across PPI networks, Nucleic Acids Research, vol.39, issue.Database, pp.295-300, 2011.
DOI : 10.1093/nar/gkq1234

K. Sjolander, R. Datta, Y. Shen, and G. Shoffner, Ortholog identification in the presence of domain architecture rearrangement, Briefings in Bioinformatics, vol.12, issue.5, pp.413-422, 2011.
DOI : 10.1093/bib/bbr036

H. Chiba and I. Uchiyama, Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score, BMC Bioinformatics, vol.15, issue.1, p.148, 2014.
DOI : 10.1371/journal.pone.0009490

T. Bitard-feildel, C. Kemena, and J. Greenwood, Domain similarity based orthology detection, BMC Bioinformatics, vol.30, issue.2, p.154, 2015.
DOI : 10.1093/bioinformatics/btt640

T. Bailey and C. Elkan, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp.28-36, 1994.

B. Dujon, Yeast evolutionary genomics, Nature Reviews Genetics, vol.104, issue.7, pp.512-524, 2010.
DOI : 10.1038/nrg2811

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

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

I. Artamonova, G. Frishman, M. Gelfand, and D. Frishman, Mining sequence annotation databanks for association patterns, Bioinformatics, vol.21, issue.Suppl 3, pp.49-57, 2005.
DOI : 10.1093/bioinformatics/bti1206

G. Project, Available at, 2015.

B. Dujon, Genome Evolution in Yeasts, 2015.
URL : https://hal.archives-ouvertes.fr/hal-00104411

T. Rolland, C. Neuvéglise, C. Sacerdot, and B. Dujon, Insertion of Horizontally Transferred Genes within Conserved Syntenic Regions of Yeast Genomes, PLoS ONE, vol.13, issue.3, p.6515, 2009.
DOI : 10.1371/journal.pone.0006515.s008

J. Gordon, K. Byrne, and K. Wolfe, Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome, PLoS Genetics, vol.55, issue.5, p.1000485, 2009.
DOI : 10.1371/journal.pgen.1000485.s003

M. Csurös and I. Miklós, Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model, Molecular Biology and Evolution, vol.26, issue.9, pp.2087-2095, 2009.
DOI : 10.1093/molbev/msp123

C. Chauve, H. Gavranovic, A. Ouangraoua, and E. Tannier, Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II, Journal of Computational Biology, vol.17, issue.9, pp.1097-1112, 2010.
DOI : 10.1089/cmb.2010.0092

URL : https://hal.archives-ouvertes.fr/hal-00681091

T. Jiang, Some Algorithmic Challenges in Genome-Wide Ortholog Assignment, Journal of Computer Science and Technology, vol.16, issue.3, pp.42-52, 2010.
DOI : 10.1007/s11390-010-9304-6

P. Williams, D. Pollock, B. Blackburne, and R. Goldstein, Assessing the Accuracy of Ancestral Protein Reconstruction Methods, PLoS Computational Biology, vol.15, issue.6, p.69, 2006.
DOI : 10.1371/journal.pcbi.0020069.st003

M. Arenas and D. Posada, The Effect of Recombination on the Reconstruction of Ancestral Sequences, Genetics, vol.184, issue.4, pp.1133-1139, 2010.
DOI : 10.1534/genetics.109.113423

N. Butzin, P. Lapierre, A. Green, K. Swithers, J. Gogarten et al., Reconstructed Ancestral Myo-Inositol-3-Phosphate Synthases Indicate That Ancestors of the Thermococcales and Thermotoga Species Were More Thermophilic than Their Descendants, PLoS ONE, vol.2, issue.12, p.84300, 2013.
DOI : 10.1371/journal.pone.0084300.s011

V. Risso, J. Gavira, E. Gaucher, and J. Sanchez-ruiz, Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins, Proteins: Structure, Function, and Bioinformatics, vol.8, issue.6, pp.887-896, 2014.
DOI : 10.1002/prot.24575

E. Pennisi and . Evolution, EVOLUTION: Building the Tree of Life, Genome by Genome, Science, vol.320, issue.5884, pp.1716-1717, 2008.
DOI : 10.1126/science.320.5884.1716

E. Pennisi, Human genome 10th anniversary. Tracing the tree of life, Science, vol.331, pp.1005-1006, 2011.

D. Durand, B. Halldorsson, and B. Vernot, A Hybrid Micro???Macroevolutionary Approach to Gene Tree Reconstruction, Journal of Computational Biology, vol.13, issue.2, pp.320-335, 2005.
DOI : 10.1089/cmb.2006.13.320

B. Vernot, M. Stolzer, A. Goldman, and D. Durand, Reconciliation with Non-Binary Species Trees, Journal of Computational Biology, vol.15, issue.8, pp.981-1006, 2008.
DOI : 10.1089/cmb.2008.0092

M. Conte, S. Gaillard, G. Droc, and C. Perin, Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants, BMC Genomics, vol.9, issue.1, p.183, 2008.
DOI : 10.1186/1471-2164-9-183

B. Sennblad and J. Lagergren, Probabilistic Orthology Analysis, Systematic Biology, vol.58, issue.4, pp.411-424, 2009.
DOI : 10.1093/sysbio/syp046

URL : http://sysbio.oxfordjournals.org/cgi/content/short/58/4/411

P. Thomas, GIGA: a simple, efficient algorithm for gene tree inference in the genomic age, BMC Bioinformatics, vol.11, issue.1, p.312, 2010.
DOI : 10.1186/1471-2105-11-312

C. Than and N. Rosenberg, Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences, Journal of Computational Biology, vol.18, issue.1, pp.1-15, 2011.
DOI : 10.1089/cmb.2010.0102

S. Kuraku, Palaeophylogenomics of the Vertebrate Ancestor--Impact of Hidden Paralogy on Hagfish and Lamprey Gene Phylogeny, Integrative and Comparative Biology, vol.50, issue.1, pp.124-129, 2010.
DOI : 10.1093/icb/icq044

S. Steinfartz, M. Weitere, and D. Tautz, Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest, Molecular Ecology, vol.13, issue.21, pp.4550-4561, 2007.
DOI : 10.1111/j.1365-294X.2007.03490.x

R. Studer and M. Robinson-rechavi, How confident can we be that orthologs are similar, but paralogs differ?, Trends in Genetics, vol.25, issue.5, pp.210-216, 2009.
DOI : 10.1016/j.tig.2009.03.004

J. Agnan, C. Korch, and C. Selitrennikoff, Cloning Heterologous Genes: Problems and Approaches, Fungal Genetics and Biology, vol.21, issue.3, pp.292-301, 1997.
DOI : 10.1006/fgbi.1997.0995

A. Thierry, V. Khanna, and S. Créno, Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes, Nature Communications, vol.25, p.6154, 2015.
DOI : 10.1093/nar/gkl758

URL : https://hal.archives-ouvertes.fr/hal-01116452

H. Yu, P. Braun, and M. Yildirim, High-Quality Binary Protein Interaction Map of the Yeast Interactome Network, Science, vol.322, issue.5898, pp.104-110, 2008.
DOI : 10.1126/science.1158684

M. Peterson, F. Chen, J. Saven, D. Roos, P. Babbitt et al., Evolutionary constraints on structural similarity in orthologs and paralogs, Protein Science, vol.33, issue.6, pp.1306-1315, 2009.
DOI : 10.1002/pro.143

K. Forslund, I. Pekkari, and E. Sonnhammer, Domain architecture conservation in orthologs, BMC Bioinformatics, vol.12, issue.1, p.326, 2011.
DOI : 10.1002/pro.143

T. Gabaldón and E. Koonin, Functional and evolutionary implications of gene orthology, Nature Reviews Genetics, vol.8, issue.5, pp.360-366, 2013.
DOI : 10.1093/nar/25.17.3389

T. Gabaldón, C. Dessimoz, J. Huxley-jones, A. Vilella, E. Sonnhammer et al., Joining forces in the quest for orthologs, Genome Biology, vol.10, issue.9, p.403, 2009.
DOI : 10.1186/gb-2009-10-9-403

K. Trachana, K. Forslund, and T. Larsson, A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation, PLoS ONE, vol.215, issue.10, p.111122, 2014.
DOI : 10.1371/journal.pone.0111122.s002