S. Amundsen, J. Fero, N. Salama, and G. Smith, Dual Nuclease and Helicase Activities of Helicobacter pylori AddAB Are Required for DNA Repair, Recombination, and Mouse Infectivity, Journal of Biological Chemistry, vol.284, issue.25, pp.16759-16766, 2009.
DOI : 10.1074/jbc.M109.005587

J. Andersson and S. Andersson, Genome degradation is an ongoing process in Rickettsia, Molecular Biology and Evolution, vol.16, issue.9, pp.1178-1191, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026208

J. Andersson and S. Andersson, Pseudogenes, Junk DNA, and the Dynamics of Rickettsia Genomes, Molecular Biology and Evolution, vol.18, issue.5, pp.829-839, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003864

L. Aravind, K. Makarova, and E. Koonin, SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories, Nucleic Acids Research, vol.28, issue.18, pp.3417-3432, 2000.
DOI : 10.1093/nar/28.18.3417

M. Ariyoshi, T. Nishino, H. Iwasaki, H. Shinagawa, and K. Morikawa, Crystal structure of the Holliday junction DNA in complex with a single RuvA tetramer, Proceedings of the National Academy of Sciences, vol.97, issue.15, pp.8257-8262, 2000.
DOI : 10.1073/pnas.140212997

S. Ayora, B. Carrasco, E. Doncel-perez, R. Lurz, and J. Alonso, Bacillus subtilis RecU protein cleaves Holliday junctions and anneals single-stranded DNA, Proceedings of the National Academy of Sciences, vol.101, issue.2, pp.452-457, 2004.
DOI : 10.1073/pnas.2533829100

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC327168

Z. Baharoglu, A. Bradley, L. Masson, M. Tsaneva, I. Michel et al., ruvA Mutants That Resolve Holliday Junctions but Do Not Reverse Replication Forks, PLoS Genetics, vol.90, issue.3, p.1000012, 2008.
DOI : 10.1371/journal.pgen.1000012.s003

C. Bandi, J. Tim, C. Genchi, and M. Bacter, Phylogeny of Wolbachia in filarial nematodes, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1413, pp.2407-2413, 1998.
DOI : 10.1098/rspb.1998.0591

G. Blanc, Reductive Genome Evolution from the Mother of Rickettsia, PLoS Genetics, vol.44, issue.1, p.14, 2007.
DOI : 10.1371/journal.pgen.0030014.st005

A. Bradley, Z. Baharoglu, A. Niewiarowski, B. Michel, and I. Tsaneva, Formation of a Stable RuvA Protein Double Tetramer Is Required for Efficient Branch Migration in Vitro and for Replication Fork Reversal in Vivo, Journal of Biological Chemistry, vol.286, issue.25, pp.22372-22383, 2011.
DOI : 10.1074/jbc.M111.233908

N. Cerveau, S. Leclercq, D. Bouchon, and R. Cordaux, Evolutionary dynamics and genomic impact of prokaryote transposable elements Evolutionary Biology: concepts, biodiversity, macroevolution and genome evolution, pp.291-312, 2011.

N. Cerveau, S. Leclercq, E. Leroy, D. Bouchon, and R. Cordaux, Short- and Long-term Evolutionary Dynamics of Bacterial Insertion Sequences: Insights from Wolbachia Endosymbionts, Genome Biology and Evolution, vol.3, issue.0, pp.1175-1186, 2011.
DOI : 10.1093/gbe/evr096

URL : https://hal.archives-ouvertes.fr/hal-00637836

S. Cole, Comparative mycobacterial genomics, Current Opinion in Microbiology, vol.1, issue.5, pp.567-571, 1998.
DOI : 10.1016/S1369-5274(98)80090-8

S. Cole, Massive gene decay in the leprosy bacillus, Nature, vol.409, issue.6823, pp.1007-1011, 2001.
DOI : 10.1038/35059006

F. Comandatore, Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes, Genome Biology and Evolution, vol.5, issue.9, 2013.
DOI : 10.1093/gbe/evt125

URL : https://hal.archives-ouvertes.fr/hal-00871812

R. Cordaux, Gene Conversion Maintains Nonfunctional Transposable Elements in an Obligate Mutualistic Endosymbiont, Molecular Biology and Evolution, vol.26, issue.8, pp.1679-1682, 2009.
DOI : 10.1093/molbev/msp093

URL : https://hal.archives-ouvertes.fr/hal-00406481

R. Cordaux, D. Bouchon, and P. Grè-ve, The impact of endosymbionts on the evolution of host sex-determination mechanisms, Trends in Genetics, vol.27, issue.8, pp.332-341, 2011.
DOI : 10.1016/j.tig.2011.05.002

URL : https://hal.archives-ouvertes.fr/hal-00626381

R. Cordaux, Intense Transpositional Activity of Insertion Sequences in an Ancient Obligate Endosymbiont, Molecular Biology and Evolution, vol.25, issue.9, pp.1889-1896, 2008.
DOI : 10.1093/molbev/msn134

URL : https://hal.archives-ouvertes.fr/hal-00319882

R. Cordaux, A. Michel-salzat, and D. Bouchon, Wolbachia infection in crustaceans: novel hosts and potential routes for horizontal transmission, Journal of Evolutionary Biology, vol.265, issue.2, pp.237-243, 2001.
DOI : 10.1046/j.1420-9101.2001.00279.x

URL : https://hal.archives-ouvertes.fr/hal-00123774

G. Cromie, Phylogenetic Ubiquity and Shuffling of the Bacterial RecBCD and AddAB Recombination Complexes, Journal of Bacteriology, vol.191, issue.16, pp.5076-5084, 2009.
DOI : 10.1128/JB.00254-09

T. Dagan, R. Blekhman, and D. Graur, The "Domino Theory" of Gene Death: Gradual and Mass Gene Extinction Events in Three Lineages of Obligate Symbiotic Bacterial Pathogens, Molecular Biology and Evolution, vol.23, issue.2, pp.310-316, 2006.
DOI : 10.1093/molbev/msj036

C. Dale, B. Wang, N. Moran, and H. Ochman, Loss of DNA Recombinational Repair Enzymes in the Initial Stages of Genome Degeneration, Molecular Biology and Evolution, vol.20, issue.8, pp.1188-1194, 2003.
DOI : 10.1093/molbev/msg138

A. Darby, Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis, Genome Research, vol.22, issue.12, pp.2467-2477, 2012.
DOI : 10.1101/gr.138420.112

URL : https://hal.archives-ouvertes.fr/hal-00771127

P. Degnan, A. Lazarus, and J. Wernegreen, Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects, Genome Research, vol.15, issue.8, pp.1023-1033, 2005.
DOI : 10.1101/gr.3771305

C. Desjardins, Genomics of Loa loa, a Wolbachia-free filarial parasite of humans, Nature Genetics, vol.9, issue.5, pp.495-500, 2013.
DOI : 10.1093/nar/gkr1014

A. Duplouy, Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources, BMC Genomics, vol.14, issue.1, p.20, 2013.
DOI : 10.1006/jmbi.2000.4042

K. Ellegaard, L. Klasson, K. Nä-slund, K. Bourtzis, and S. Andersson, Comparative Genomics of Wolbachia and the Bacterial Species Concept, PLoS Genetics, vol.286, issue.1, p.1003381, 2013.
DOI : 10.1371/journal.pgen.1003381.s017

B. Finlay and S. Falkow, Common themes in microbial pathogenicity revisited, Microbiol Mol Biol Rev, vol.61, pp.136-169, 1997.

J. Foster, The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode, PLoS Biology, vol.15, issue.1450, p.121, 2005.
DOI : 10.1371/journal.pbio.0030121.t003

A. Fry and J. Wernegreen, The roles of positive and negative selection in the molecular evolution of insect endosymbionts, Gene, vol.355, pp.1-10, 2005.
DOI : 10.1016/j.gene.2005.05.021

Y. Fujiwara, K. Mayanagi, and K. Morikawa, Functional significance of octameric RuvA for a branch migration complex from Thermus thermophilus, Biochemical and Biophysical Research Communications, vol.366, issue.2, pp.426-431, 2008.
DOI : 10.1016/j.bbrc.2007.11.149

H. Fuxelius, A. Darby, N. Cho, and S. Andersson, Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction, Genome Biology, vol.9, issue.2, p.42, 2008.
DOI : 10.1186/gb-2008-9-2-r42

R. Gil, The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes, Proceedings of the National Academy of Sciences, vol.100, issue.16, pp.9388-9393, 2003.
DOI : 10.1073/pnas.1533499100

C. Godel, The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets, The FASEB Journal, vol.26, issue.11, pp.4650-4661, 2012.
DOI : 10.1096/fj.12-205096

L. Gó-mez-valero, A. Latorre, and F. Silva, The Evolutionary Fate of Nonfunctional DNA in the Bacterial Endosymbiont Buchnera aphidicola, Molecular Biology and Evolution, vol.21, issue.11, pp.2172-2181, 2004.
DOI : 10.1093/molbev/msh232

T. Itoh, W. Martin, and M. Nei, Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.12944-12948, 2002.
DOI : 10.1073/pnas.192449699

B. Kent and S. Bordenstein, Phage WO of Wolbachia: lambda of the endosymbiont world, Trends in Microbiology, vol.18, issue.4, pp.173-181, 2010.
DOI : 10.1016/j.tim.2009.12.011

B. Kent, Complete Bacteriophage Transfer in a Bacterial Endosymbiont (Wolbachia) Determined by Targeted Genome Capture, Genome Biology and Evolution, vol.3, issue.0, 2011.
DOI : 10.1093/gbe/evr007

L. Klasson, Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group, Molecular Biology and Evolution, vol.25, issue.9, pp.1877-1887, 2008.
DOI : 10.1093/molbev/msn133

L. Klasson, The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans, Proceedings of the National Academy of Sciences, vol.106, issue.14, pp.57225-57230, 2009.
DOI : 10.1073/pnas.0810753106

E. Koonin, A. Mushegian, and P. Bork, Non-orthologous gene displacement, Trends in Genetics, vol.12, issue.9, pp.334-336, 1996.
DOI : 10.1016/0168-9525(96)20010-1

S. Kowalczykowski, Initiation of genetic recombination and recombination-dependent replication, Trends in Biochemical Sciences, vol.25, issue.4, pp.156-165, 2000.
DOI : 10.1016/S0968-0004(00)01569-3

L. Masson, M. Baharoglu, Z. Michel, and B. , mutants specifically impaired for replication fork reversal, Molecular Microbiology, vol.14, issue.2, pp.537-548, 2008.
DOI : 10.1111/j.1365-2958.2008.06431.x

S. Leclercq, I. Giraud, and R. Cordaux, Remarkable Abundance and Evolution of Mobile Group II Introns in Wolbachia Bacterial Endosymbionts, Molecular Biology and Evolution, vol.28, issue.1, pp.685-697, 2011.
DOI : 10.1093/molbev/msq238

URL : https://hal.archives-ouvertes.fr/hal-00551571

N. Lo, Taxonomic status of the intracellular bacterium Wolbachia pipientis, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.57, issue.3, pp.654-657, 2007.
DOI : 10.1099/ijs.0.64515-0

D. Martin, RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, pp.2462-2463, 2010.
DOI : 10.1093/bioinformatics/btq467

P. Mavingui, Whole-Genome Sequence of Wolbachia Strain wAlbB, an Endosymbiont of Tiger Mosquito Vector Aedes albopictus, Journal of Bacteriology, vol.194, issue.7, 2012.
DOI : 10.1128/JB.00036-12

URL : https://hal.archives-ouvertes.fr/halsde-00723025

K. Mayanagi, Y. Fujiwara, T. Miyata, and K. Morikawa, Electron microscopic single particle analysis of a tetrameric RuvA/RuvB/Holliday junction DNA complex, Biochemical and Biophysical Research Communications, vol.365, issue.2, pp.273-278, 2008.
DOI : 10.1016/j.bbrc.2007.10.165

J. Mccutcheon and N. Moran, Extreme genome reduction in symbiotic bacteria, Nature Reviews Microbiology, vol.186, pp.13-26, 2012.
DOI : 10.1038/nrmicro2670

T. Meddows, A. Savory, and R. Lloyd, RecG helicase promotes DNA double-strand break repair, Molecular Microbiology, vol.281, issue.1, pp.119-132, 2004.
DOI : 10.1111/j.1365-2958.2003.03970.x

I. Mehr and H. Seifert, pilin antigenic variation, DNA transformation and DNA repair, Molecular Microbiology, vol.95, issue.4, pp.697-710, 1998.
DOI : 10.1046/j.1365-2958.1998.01089.x

A. Mendonç-a, R. Alves, and J. Pereira-leal, Loss of Genetic Redundancy in Reductive Genome Evolution, PLoS Computational Biology, vol.278, issue.2, p.1001082, 2011.
DOI : 10.1371/journal.pcbi.1001082.s001

A. Mira, H. Ochman, and N. Moran, Deletional bias and the evolution of bacterial genomes, Trends in Genetics, vol.17, issue.10, pp.589-596, 2001.
DOI : 10.1016/S0168-9525(01)02447-7

N. Moran, Accelerated evolution and Muller's ratchet in endosymbiotic bacteria, Proc Natl Acad Sci U S A, vol.93, pp.2973-2878, 1996.

N. Moran, J. Mccutcheon, and A. Nakabachi, Genomics and Evolution of Heritable Bacterial Symbionts, Annual Review of Genetics, vol.42, issue.1, pp.165-190, 2008.
DOI : 10.1146/annurev.genet.41.110306.130119

N. Moran, H. Mclaughlin, and R. Sorek, The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria, Science, vol.323, issue.5912, pp.379-382, 2009.
DOI : 10.1126/science.1167140

N. Moran and M. A. , The process of genome shrinkage in the obligate symbiont Buchnera aphidicola, Genome Biol, vol.2, p.54, 2001.

N. Moran and G. Plague, Genomic changes following host restriction in bacteria, Current Opinion in Genetics & Development, vol.14, issue.6, pp.627-633, 2004.
DOI : 10.1016/j.gde.2004.09.003

A. Moya, J. Pereto, R. Gil, and A. Latorre, Learning how to live together: genomic insights into prokaryote???animal symbioses, Nature Reviews Genetics, vol.34, issue.3, pp.218-229, 2008.
DOI : 10.1038/nrg2319

A. Nilsson, From The Cover: Bacterial genome size reduction by experimental evolution, Proceedings of the National Academy of Sciences, vol.102, issue.34, pp.12112-12116, 2005.
DOI : 10.1073/pnas.0503654102

T. Nishino, M. Ariyoshi, H. Iwasaki, H. Shinagawa, and K. Morikawa, Functional analyses of the domain structure in the Holliday junction binding protein RuvA, Structure, vol.6, issue.1, pp.11-21, 1998.
DOI : 10.1016/S0969-2126(98)00003-3

T. Nishino, Modulation of RuvB function by the mobile domain III of the holliday junction recognition protein RuvA, Journal of Molecular Biology, vol.298, issue.3, pp.407-416, 2000.
DOI : 10.1006/jmbi.2000.3675

H. Ogata, Mechanisms of Evolution in Rickettsia conorii and R. prowazekii, Science, vol.293, issue.5537, pp.2093-2098, 2001.
DOI : 10.1126/science.1061471

H. Ogata, K. Suhre, and J. Claverie, Discovery of protein-coding palindromic repeats in Wolbachia, Trends in Microbiology, vol.13, issue.6, pp.253-255, 2005.
DOI : 10.1016/j.tim.2005.03.013

T. Ohta and J. Gillespie, Development of Neutral and Nearly Neutral Theories, Theoretical Population Biology, vol.49, issue.2, pp.128-142, 1996.
DOI : 10.1006/tpbi.1996.0007

V. Pé-rez-brocal, A Small Microbial Genome: The End of a Long Symbiotic Relationship?, Science, vol.314, issue.5797, pp.312-313, 2006.
DOI : 10.1126/science.1130441

G. Plague, H. Dunbar, P. Tran, and N. Moran, Extensive Proliferation of Transposable Elements in Heritable Bacterial Symbionts, Journal of Bacteriology, vol.190, issue.2, pp.777-779, 2008.
DOI : 10.1128/JB.01082-07

J. Prabu, RuvA, a protein involved in recombination, Acta Crystallographica Section F Structural Biology and Crystallization Communications, vol.62, issue.8, pp.731-734, 2006.
DOI : 10.1107/S1744309106024791

J. Prabu, Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1794, issue.7, pp.1001-1009, 2009.
DOI : 10.1016/j.bbapap.2009.04.003

C. Privezentzev, A. Keeley, B. Sigala, and I. Tsaneva, The Role of RuvA Octamerization for RuvAB Function in Vitro and in Vivo, Journal of Biological Chemistry, vol.280, issue.5, pp.3365-3375, 2005.
DOI : 10.1074/jbc.M409256200

J. Rafferty, Crystal Structure of DNA Recombination Protein RuvA and a Model for Its Binding to the Holliday Junction, Science, vol.274, issue.5286, pp.415-421, 1996.
DOI : 10.1126/science.274.5286.415

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. Roe, Crystal Structure of an Octameric RuvA???Holliday Junction Complex, Molecular Cell, vol.2, issue.3, pp.361-372, 1998.
DOI : 10.1016/S1097-2765(00)80280-4

S. Saha, Survey of Endosymbionts in the Diaphorina citri Metagenome and Assembly of a Wolbachia wDi Draft Genome, PLoS ONE, vol.22, issue.11, p.50067, 2012.
DOI : 10.1371/journal.pone.0050067.s010

S. Salzberg, D. Puiu, D. Sommer, V. Nene, and N. Lee, Genome Sequence of the Wolbachia Endosymbiont of Culex quinquefasciatus JHB, Journal of Bacteriology, vol.191, issue.5, p.1725, 2009.
DOI : 10.1128/JB.01731-08

F. Silva, A. Latorre, and A. Moya, Genome size reduction through multiple events of gene disintegration in Buchnera APS, Trends in Genetics, vol.17, issue.11, pp.615-618, 2001.
DOI : 10.1016/S0168-9525(01)02483-0

F. Silva, A. Latorre, and A. Moya, Why are the genomes of endosymbiotic bacteria so stable?, Trends in Genetics, vol.19, issue.4, pp.176-180, 2003.
DOI : 10.1016/S0168-9525(03)00041-6

S. Siozios, Draft Genome Sequence of the Wolbachia Endosymbiont of Drosophila suzukii, Genome Announcements, vol.1, issue.1, pp.32-45, 2013.
DOI : 10.1128/genomeA.00032-13

I. Tamas, 50 Million Years of Genomic Stasis in Endosymbiotic Bacteria, Science, vol.296, issue.5577, pp.2376-2379, 2002.
DOI : 10.1126/science.1071278

I. Tamas, Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.14934-14939, 2008.
DOI : 10.1073/pnas.0806554105

K. Tamura, MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.
DOI : 10.1093/molbev/msr121

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203626

C. Toft and S. Andersson, Evolutionary microbial genomics: insights into bacterial host adaptation, Nature Reviews Genetics, vol.462, issue.7, pp.465-475, 2010.
DOI : 10.1038/nrg2798

T. Treangen, A. Abraham, M. Touchon, and E. Rocha, Genesis, effects and fates of repeats in prokaryotic genomes, FEMS Microbiology Reviews, vol.33, issue.3, pp.539-571, 2009.
DOI : 10.1111/j.1574-6976.2009.00169.x

J. Van-leuven and J. Mccutcheon, An AT Mutational Bias in the Tiny GC-Rich Endosymbiont Genome of Hodgkinia, Genome Biology and Evolution, vol.4, issue.1, pp.24-27, 2012.
DOI : 10.1093/gbe/evr125

A. Walker and G. Langridge, Does my genome look big in this?, Nature Reviews Microbiology, vol.11, issue.12, pp.878-879, 2008.
DOI : 10.1128/JB.01949-07

J. Wernegreen, For better or worse: genomic consequences of intracellular mutualism and parasitism, Current Opinion in Genetics & Development, vol.15, issue.6, pp.572-583, 2005.
DOI : 10.1016/j.gde.2005.09.013

J. Wernegreen and D. Funk, Mutation Exposed: A Neutral Explanation for Extreme Base Composition of an Endosymbiont Genome, Journal of Molecular Evolution, vol.13, issue.1, pp.849-858, 2004.
DOI : 10.1007/s00239-003-0192-z

J. Wernegreen and N. Moran, Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes, Molecular Biology and Evolution, vol.16, issue.1, pp.83-97, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026040

J. Werren, L. Baldo, and M. Clark, Wolbachia: master manipulators of invertebrate biology, Nature Reviews Microbiology, vol.12, issue.10, pp.741-751, 2008.
DOI : 10.1099/ijs.0.64515-0

J. Werren and J. Bartos, Recombination in Wolbachia, Current Biology, vol.11, issue.6, pp.431-435, 2001.
DOI : 10.1016/S0960-9822(01)00101-4

M. Woolfit and L. Bromham, Increased Rates of Sequence Evolution in Endosymbiotic Bacteria and Fungi with Small Effective Population Sizes, Molecular Biology and Evolution, vol.20, issue.9, pp.1545-1555, 2003.
DOI : 10.1093/molbev/msg167

M. Wu, Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements, PLoS Biology, vol.265, issue.3, p.327, 2004.
DOI : 10.1371/journal.pbio.0020069.st009

K. Yamada, Crystal Structure of the RuvA-RuvB Complex, Molecular Cell, vol.10, issue.3, pp.671-681, 2002.
DOI : 10.1016/S1097-2765(02)00641-X

Z. Yang, Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution, Molecular Biology and Evolution, vol.15, issue.5, pp.568-573, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025957

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088

Z. Yang, W. Wong, and R. Nielsen, Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection, Molecular Biology and Evolution, vol.22, issue.4, pp.1107-1118, 2005.
DOI : 10.1093/molbev/msi097

J. Zhang, R. Nielsen, and Z. Yang, Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level, Molecular Biology and Evolution, vol.22, issue.12, pp.2472-2479, 2005.
DOI : 10.1093/molbev/msi237

J. Zuñ-iga-castillo, D. Romero, and J. Martínez-salazar, The Recombination Genes addAB Are Not Restricted to Gram-Positive Bacteria: Genetic Analysis of the Recombination Initiation Enzymes RecF and AddAB in Rhizobium etli, Journal of Bacteriology, vol.186, issue.23, pp.7905-7913, 2004.
DOI : 10.1128/JB.186.23.7905-7913.2004