G. Szöll?si, B. Boussau, S. Abby, E. Tannier, and V. Daubin, Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences, vol.109, issue.43, pp.17513-17518, 2012.
DOI : 10.1073/pnas.1202997109

J. Sjöstrand, A. Tofigh, V. Daubin, L. Arvestad, B. Sennblad et al., A Bayesian Method for Analyzing Lateral Gene Transfer, Systematic Biology, vol.63, issue.3, pp.409-420
DOI : 10.1093/sysbio/syu007

B. Boussau and V. Daubin, Genomes as documents of evolutionary history, Trends in Ecology & Evolution, vol.25, issue.4, pp.224-256
DOI : 10.1016/j.tree.2009.09.007
URL : https://hal.archives-ouvertes.fr/hal-00539397

C. Chauve, N. El-mabrouk, L. Guéguen, M. Semeria, and E. Tannier, Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later, Model Algorithms Genome Evol, pp.47-62
DOI : 10.1007/978-1-4471-5298-9_4

A. Sturtevant and T. Dobzhansky, Inversions in the Third Chromosome of Wild Races of Drosophila Pseudoobscura, and Their Use in the Study of the History of the Species, Proceedings of the National Academy of Sciences, vol.22, issue.7, pp.448-50, 1936.
DOI : 10.1073/pnas.22.7.448

D. Sankoff, Mechanisms of genome evolution: models and inference. Bulletin of international statistical institute, pp.461-475, 1989.

G. Bourque, P. Pevzner, and G. Tesler, Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes, Genome Research, vol.14, issue.4
DOI : 10.1101/gr.1975204

M. Muffato, A. Louis, C. Poisnel, R. Crollius, and H. , Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes, Bioinformatics, vol.26, issue.8, pp.1119-1140, 2010.
DOI : 10.1093/bioinformatics/btq079

S. Bérard, C. Galien, B. Boussau, G. Szollosi, V. Daubin et al., Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.28, issue.18, pp.382-388
DOI : 10.1093/bioinformatics/bts374

Y. Gagnon and M. Blanchette, El-Mabrouk N: A flexible ancestral genome reconstruction method based on gapped adjacencies, BMC Bioinformatics, vol.13, issue.1, p.4, 2012.

R. Durrett, R. Nielsen, and T. York, Bayesian Estimation of Genomic Distance, Genetics, vol.166, issue.1, pp.621-629, 2004.
DOI : 10.1534/genetics.166.1.621

B. Larget, J. Kadane, and D. Simon, A bayesian approach to the estimation of ancestral genome arrangements. Molecular phylogenetics and evolution, pp.214-223, 2005.

J. Ma, A probabilistic framework for inferring ancestral genomic orders, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.179-184
DOI : 10.1109/BIBM.2010.5706559

Y. Zhang, F. Hu, and J. Tang, A mixture framework for inferring ancestral gene orders, BMC Genomics, vol.13, issue.Suppl 1, p.7
DOI : 10.1186/1471-2105-11-S1-S54

Y. Lin, F. Hu, J. Tang, and B. Moret, MAXIMUM LIKELIHOOD PHYLOGENETIC RECONSTRUCTION FROM HIGH-RESOLUTION WHOLE-GENOME DATA AND A TREE OF 68 EUKARYOTES, Biocomputing 2013, pp.285-96
DOI : 10.1142/9789814447973_0028

N. Yang, F. Hu, L. Zhou, and J. Tang, Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches, PLoS ONE, vol.65, issue.3, p.108796
DOI : 10.1371/journal.pone.0108796.t004

G. Blin, C. Chauve, G. Fertin, R. Rizzi, and S. Vialette, Comparing Genomes with Duplications: A Computational Complexity Point of View, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.4, pp.523-534, 2007.
DOI : 10.1109/TCBB.2007.1069
URL : https://hal.archives-ouvertes.fr/hal-00417720

. Semeria, Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies, BMC Bioinformatics, vol.16, issue.Suppl 14, p.5, 2015.
DOI : 10.1186/1471-2105-16-S14-S5
URL : https://hal.archives-ouvertes.fr/hal-01179596

C. Gallut and V. Barriel, Cladistic coding of genomic maps, Cladistics, vol.99, issue.5, pp.526-536, 2002.
DOI : 10.1016/0025-5564(87)90074-5

J. Ma?uch, M. Patterson, R. Wittler, C. Chauve, and E. Tannier, Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, vol.2012, issue.13, p.11

Y. Wu, M. Rasmussen, and M. Kellis, Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny, Molecular Biology and Evolution, vol.29, issue.2, pp.689-705
DOI : 10.1093/molbev/msr222

J. Ma, A. Ratan, and B. Raney, DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications, Journal of Computational Biology, vol.15, issue.8, pp.1007-1027, 2008.
DOI : 10.1089/cmb.2008.0069
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822

L. Guéguen, S. Gaillard, B. Boussau, M. Gouy, M. Groussin et al., Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution, Molecular Biology and Evolution, vol.30, issue.8, pp.301745-1750
DOI : 10.1093/molbev/mst097

Q. Peng, P. Pevzner, and G. Tesler, The Fragile Breakage versus Random Breakage Models of Chromosome Evolution, PLoS Computational Biology, vol.65, issue.2, p.14, 2006.
DOI : 10.1371/journal.pcbi.0020014.sg002

C. Berthelot, M. Muffato, and J. Abecassis, Roest Crollius H: The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions, Cell Reports, vol.10, pp.1-12, 2015.

B. Boussau, G. Szöll?si, L. Duret, M. Gouy, and V. Daubin, Genome-scale coestimation of species and gene trees, Genome Research, vol.23, issue.2, pp.323-330, 2013.
DOI : 10.1101/gr.141978.112
URL : https://hal.archives-ouvertes.fr/hal-00750148

D. Pollard, V. Iyer, A. Moses, and M. Eisen, Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting, PLoS Genetics, vol.5, issue.10, p.173, 2006.
DOI : 10.1371/journal.pgen.0020173.st001

F. Hu, J. Zhou, L. Zhou, and J. Tang, Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.11, issue.4, pp.59631-59632
DOI : 10.1109/TCBB.2014.2309602

C. Dewey, Positional orthology: putting genomic evolutionary relationships into context, Briefings in Bioinformatics, vol.12, issue.5, pp.401-413
DOI : 10.1093/bib/bbr040
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178058

O. Mahmudi, J. Sjostrand, B. Sennblad, and J. Lagergren, Genome-wide probabilistic reconciliation analysis across vertebrates, BMC Bioinformatics, vol.14, issue.Suppl 15, p.10
DOI : 10.1038/nprot.2008.211
URL : http://doi.org/10.1186/1471-2105-14-s15-s10

M. Patterson, G. Szöll?si, V. Daubin, and E. Tannier, Lateral gene transfer, rearrangement, reconciliation, BMC Bioinformatics, vol.14, issue.Suppl 15, p.4
DOI : 10.1137/0128004
URL : https://hal.archives-ouvertes.fr/hal-00873233

Z. Yang, Among-site rate variation and its impact on phylogenetic analyses, Trends in Ecology & Evolution, vol.11, issue.9, pp.367-372, 1996.
DOI : 10.1016/0169-5347(96)10041-0