B. Michel, G. Grompone, M. Flores, and V. Bidnenko, Multiple pathways process stalled replication forks, Proceedings of the National Academy of Sciences, vol.101, issue.35, pp.12783-12788, 2004.
DOI : 10.1073/pnas.0401586101

K. Perals, H. Capiaux, J. Vincourt, J. Louarn, and D. Sherratt, Interplay between recombination, cell division and chromosome structure during chromosome dimer resolution in Escherichia coli, Molecular Microbiology, vol.29, issue.4, pp.904-913, 2001.
DOI : 10.1046/j.1365-2958.2001.02277.x

N. Barton and B. Charlesworth, Why Sex and Recombination?, Science, vol.281, issue.5385, pp.1986-1990, 1998.
DOI : 10.1126/science.281.5385.1986

E. Feil, E. Holmes, D. Bessen, M. Chan, and N. Day, Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences, Proceedings of the National Academy of Sciences, vol.98, issue.1, pp.182-187, 2001.
DOI : 10.1073/pnas.98.1.182

H. Ochman, E. Lerat, and V. Daubin, Examining bacterial species under the specter of gene transfer and exchange, Proceedings of the National Academy of Sciences, vol.102, issue.Supplement 1, pp.6595-6599, 2005.
DOI : 10.1073/pnas.0502035102
URL : https://hal.archives-ouvertes.fr/hal-00427799

R. Hendrix, M. Smith, R. Burns, M. Ford, and G. Hatfull, Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage, Proceedings of the National Academy of Sciences, vol.96, issue.5, pp.2192-2197, 1999.
DOI : 10.1073/pnas.96.5.2192

R. Juhala, M. Ford, R. Duda, A. Youlton, and G. Hatfull, Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages, Journal of Molecular Biology, vol.299, issue.1, pp.27-51, 2000.
DOI : 10.1006/jmbi.2000.3729

J. Martinsohn, M. Radman, and M. Petit, The ?? Red Proteins Promote Efficient Recombination between Diverged Sequences: Implications for Bacteriophage Genome Mosaicism, PLoS Genetics, vol.97, issue.5, p.1000065, 2008.
DOI : 10.1371/journal.pgen.1000065.s008
URL : https://hal.archives-ouvertes.fr/inserm-00496049

D. Botstein, A THEORY OF MODULAR EVOLUTION FOR BACTERIOPHAGES, Annals of the New York Academy of Sciences, vol.17, issue.1 Genetic Varia, 1980.
DOI : 10.1016/S0022-2836(75)80127-6

L. Bobay, E. Rocha, and M. Touchon, The Adaptation of Temperate Bacteriophages to Their Host Genomes, Molecular Biology and Evolution, vol.30, issue.4, pp.737-751, 2013.
DOI : 10.1093/molbev/mss279
URL : https://hal.archives-ouvertes.fr/pasteur-01374945

A. Campbell, D. Botstein, R. Hendrix, J. Roberts, F. Stahl et al., Evolution of the lambdoid phages, Lambda II. Cold Spring Harbor, pp.365-380, 1983.

S. Casjens and R. Hendrix, Comments on the arrangement of the morphogenetic genes of bacteriophage lambda, Journal of Molecular Biology, vol.90, issue.1, pp.20-25, 1974.
DOI : 10.1016/0022-2836(74)90253-8

A. Kashiwagi and T. Yomo, Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Q?? and Escherichia coli, PLoS Genetics, vol.26, issue.8, p.1002188, 2011.
DOI : 10.1371/journal.pgen.1002188.s005

L. Petersen, J. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, Genes under positive selection in Escherichia coli, Genome Research, vol.17, issue.9, pp.1336-1343, 2007.
DOI : 10.1101/gr.6254707

S. Paterson, T. Vogwill, A. Buckling, R. Benmayor, and A. Spiers, Antagonistic coevolution accelerates molecular evolution, Nature, vol.16, issue.7286, pp.275-278, 2010.
DOI : 10.1038/nature08798

M. Weinbauer, Ecology of prokaryotic viruses, FEMS Microbiology Reviews, vol.28, issue.2, pp.127-181, 2004.
DOI : 10.1016/j.femsre.2003.08.001

G. Smith, R. Hendrix, J. Roberts, F. Stahl, and R. Weisberg, General Recombination, Lambda II. Cold Spring Harbor, pp.175-210, 1983.

L. Enquist and A. Skalka, Replication of bacteriophage ?? DNA dependent on the function of host and viral genes, Journal of Molecular Biology, vol.75, issue.2, pp.185-212, 1973.
DOI : 10.1016/0022-2836(73)90016-8

A. Kuzminov, Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda, Microbiol Mol Biol Rev, vol.63, pp.751-813, 1999.

M. Maresca, A. Erler, J. Fu, A. Friedrich, and Y. Zhang, Single-stranded heteroduplex intermediates in ?? Red homologous recombination, BMC Molecular Biology, vol.11, issue.1, p.54, 2010.
DOI : 10.1186/1471-2199-11-54

R. Unger and A. Clark, Interaction of the recombination pathways of bacteriophage ?? and its host Escherichia coli K12: Effects on exonuclease V activity, Journal of Molecular Biology, vol.70, issue.3, pp.539-548, 1972.
DOI : 10.1016/0022-2836(72)90558-X

L. Iyer, E. Koonin, and L. Aravind, Classification and evolutionary history of the single-strand annealing proteins, BMC Genomics, vol.3, issue.1, p.8, 2002.
DOI : 10.1186/1471-2164-3-8

A. Lopes, J. Amarir-bouhram, G. Faure, M. Petit, and R. Guerois, Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs, Nucleic Acids Research, vol.38, issue.12, pp.3952-3962, 2010.
DOI : 10.1093/nar/gkq096

R. Myers and F. Stahl, chi and the RecBC D Enzyme of Escherichia Coli, Annual Review of Genetics, vol.28, issue.1, pp.49-70, 1994.
DOI : 10.1146/annurev.ge.28.120194.000405

M. Dillingham and S. Kowalczykowski, RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks, Microbiology and Molecular Biology Reviews, vol.72, issue.4, pp.642-671, 2008.
DOI : 10.1128/MMBR.00020-08

E. Karoui, M. Biaudet, V. Schbath, S. Gruss, and A. , Characteristics of Chi distribution on different bacterial genomes, Research in Microbiology, vol.150, issue.9-10, pp.579-587, 1999.
DOI : 10.1016/S0923-2508(99)00132-1

D. Halpern, H. Chiapello, S. Schbath, S. Robin, and C. Hennequet-antier, Identification of DNA Motifs Implicated in Maintenance of Bacterial Core Genomes by Predictive Modeling, PLoS Genetics, vol.95, issue.9, pp.1614-1621, 2007.
DOI : 10.1371/journal.pgen.0030153.st005
URL : https://hal.archives-ouvertes.fr/hal-01197542

A. Kuzminov, E. Schabtach, and F. Stahl, Chi sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating exoV activity of RecBCD nuclease, Embo J, vol.13, pp.2764-2776, 1994.

D. Anderson and S. Kowalczykowski, Reconstitution of an SOS Response Pathway, Cell, vol.95, issue.7, pp.975-979, 1998.
DOI : 10.1016/S0092-8674(00)81721-3

I. Kobayashi, Selfishness and death: raison d'??tre of restriction, recombination and mitochondria, Trends in Genetics, vol.14, issue.9, pp.368-374, 1998.
DOI : 10.1016/S0168-9525(98)01532-7

J. Bull, M. Badgett, R. Springman, and I. Molineux, GENOME PROPERTIES AND THE LIMITS OF ADAPTATION IN BACTERIOPHAGES, Evolution, vol.61, issue.4, pp.692-701, 2004.
DOI : 10.1007/BF01237884

M. De-paepe and F. Taddei, Viruses' Life History: Towards a Mechanistic Basis of a Trade-Off between Survival and Reproduction among Phages, PLoS Biology, vol.258, issue.7, p.193, 2006.
DOI : 10.1371/journal.pbio.0040193.t001
URL : https://hal.archives-ouvertes.fr/inserm-00080125

F. Capaldo, G. Ramsey, and S. Barbour, Analysis of Growth of Recombination-Deficient Strains of Escherichia-Coli-K-12, J Bacteriol, vol.118, pp.242-249, 1974.

K. Murphy, Phage Recombinases and Their Applications, Advances in Virus Research Bacteriophages, Pt B, vol.83, issue.83, pp.367-414, 2012.
DOI : 10.1016/B978-0-12-394438-2.00008-6

N. Thomson, S. Baker, D. Pickard, M. Fookes, and M. Anjum, The Role of Prophage-like Elements in the Diversity of Salmonella enterica Serovars, Journal of Molecular Biology, vol.339, issue.2, pp.279-300, 2004.
DOI : 10.1016/j.jmb.2004.03.058

N. Handa, A. Ichige, K. Kusano, and I. Kobayashi, Cellular Responses to Postsegregational Killing by Restriction-Modification Genes, Journal of Bacteriology, vol.182, issue.8, pp.2218-2229, 2000.
DOI : 10.1128/JB.182.8.2218-2229.2000

P. Noirot, R. Gupta, C. Radding, and R. Kolodner, Hallmarks of homology recognition by RecA-like recombinases are exhibited by the unrelated Escherichia coli RecT protein, The EMBO Journal, vol.22, issue.2, pp.324-334, 2003.
DOI : 10.1093/emboj/cdg027

E. Rocha, E. Cornet, and B. Michel, Comparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems, PLoS Genetics, vol.188, issue.2, p.15, 2005.
DOI : 0378-1097(2000)188[0209:COGAGC]2.0.CO;2

S. Sourice, V. Biaudet, M. Karoui, S. Ehrlich, and A. Gruss, Identification of the Chi site of Haemophilus influenzae as several sequences related to the Escherichia coli Chi site, Molecular Microbiology, vol.27, issue.5, pp.1021-1029, 1998.
DOI : 10.1006/plas.1994.1011

H. Myung and R. Calendar, The old exonuclease of bacteriophage P2., Journal of Bacteriology, vol.177, issue.3, pp.497-501, 1995.
DOI : 10.1128/jb.177.3.497-501.1995

J. Bouchard and S. Moineau, Lactococcal Phage Genes Involved in Sensitivity to AbiK and Their Relation to Single-Strand Annealing Proteins, Journal of Bacteriology, vol.186, issue.11, pp.3649-3652, 2004.
DOI : 10.1128/JB.186.11.3649-3652.2004

M. Ohnishi, K. Kurokawa, and T. Hayashi, Diversification of Escherichia coli genomes: are bacteriophages the major contributors?, Trends in Microbiology, vol.9, issue.10, pp.481-485, 2001.
DOI : 10.1016/S0966-842X(01)02173-4

D. Rasko, D. Webster, J. Sahl, A. Bashir, and N. Boisen, Strain Causing an Outbreak of Hemolytic???Uremic Syndrome in Germany, New England Journal of Medicine, vol.365, issue.8, pp.709-717, 2011.
DOI : 10.1056/NEJMoa1106920

K. Oliver, P. Degnan, M. Hunter, and N. Moran, Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism, Science, vol.325, issue.5943, pp.992-994, 2009.
DOI : 10.1126/science.1174463

F. Stahl, Chi: a little sequence controls a big enzyme, Genetics, vol.170, pp.487-493, 2005.

C. Canchaya, G. Fournous, and H. Brussow, The impact of prophages on bacterial chromosomes, Molecular Microbiology, vol.413, issue.1, pp.9-18, 2004.
DOI : 10.1111/j.1365-2958.2004.04113.x

R. Hendrix and S. Casjens, Bacteriophage Lambda and its Genetic Neighborhood, The Bacteriophages, pp.409-447, 2006.

M. Bailly-bechet, M. Vergassola, and E. Rocha, Causes for the intriguing presence of tRNAs in phages, Genome Research, vol.17, issue.10, pp.1486-1495, 2007.
DOI : 10.1101/gr.6649807
URL : https://hal.archives-ouvertes.fr/hal-00434705

B. Davis, E. Lawson, M. Sandkvist, A. Ali, and S. Sozhamannan, Convergence of the Secretory Pathways for Cholera Toxin and the Filamentous Phage, CTX, Science, vol.288, issue.5464, pp.333-335, 2000.
DOI : 10.1126/science.288.5464.333

S. Brown, Do all parasites manipulate their hosts?, Behavioural Processes, vol.68, issue.3, pp.237-240, 2005.
DOI : 10.1016/j.beproc.2004.08.015

D. Fouts, Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Research, vol.34, issue.20, pp.5839-5851, 2006.
DOI : 10.1093/nar/gkl732

Y. Zhou, Y. Liang, K. Lynch, J. Dennis, and D. Wishart, PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.39, issue.suppl, pp.347-352, 2011.
DOI : 10.1093/nar/gkr485

G. Lima-mendez, J. Van-helden, A. Toussaint, and R. Leplae, Prophinder: a computational tool for prophage prediction in prokaryotic genomes, Bioinformatics, vol.24, issue.6, pp.863-865, 2008.
DOI : 10.1093/bioinformatics/btn043

M. Touchon and E. Rocha, Causes of Insertion Sequences Abundance in Prokaryotic Genomes, Molecular Biology and Evolution, vol.24, issue.4, pp.969-981, 2007.
DOI : 10.1093/molbev/msm014

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

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

M. Remmert, A. Biegert, A. Hauser, and J. Soding, HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nature Methods, vol.11, issue.2, pp.173-175, 2012.
DOI : 10.1006/jmbi.1993.1626

S. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

S. Schbath and M. Hoebeke, R'MES: A Tool to Find Motifs with a Significantly Unexpected Frequency in Biological Sequences, 2011.
DOI : 10.1142/9789814327732_0002

E. Rocha and A. Danchin, Base composition bias might result from competition for metabolic resources, Trends in Genetics, vol.18, issue.6, pp.291-294, 2002.
DOI : 10.1016/S0168-9525(02)02690-2

S. Schbath, B. Prum, and T. Ed, Exceptional Motifs in Different Markov Chain Models for a Statistical Analysis of DNA Sequences, Journal of Computational Biology, vol.2, issue.3, pp.417-437, 1995.
DOI : 10.1089/cmb.1995.2.417

K. Cheng and G. Smith, Cutting of chi-like sequences by the RecBCD enzyme of Escherichia coli, Journal of Molecular Biology, vol.194, issue.4, pp.747-750, 1987.
DOI : 10.1016/0022-2836(87)90252-X

P. Novichkov, M. Omelchenko, M. Gelfand, A. Mironov, and Y. Wolf, Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution, Journal of Bacteriology, vol.186, issue.19, pp.6575-6585, 2004.
DOI : 10.1128/JB.186.19.6575-6585.2004

A. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010.
DOI : 10.1186/1471-2148-10-210

H. Schmidt, K. Strimmer, M. Vingron, and A. Von-haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002.
DOI : 10.1093/bioinformatics/18.3.502