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.448-450, 1936.
DOI : 10.1073/pnas.22.7.448

A. Sturtevant and C. Tan, The comparative genetics ofDrosophila pseudoobscura andD. melanogaster, Journal of Genetics, vol.34, issue.3, pp.415-432, 1937.
DOI : 10.1007/BF02982303

G. Fertin, A. Labarre, I. Rusu, E. Tannier, and S. Vialette, Combinatorics of genome rearrangements, 2009.
DOI : 10.7551/mitpress/9780262062824.001.0001
URL : https://hal.archives-ouvertes.fr/hal-00416453

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
DOI : 10.1142/9789814447973_0028

E. Zuckerkandl and L. Pauling, Molecules as documents of evolutionary history, Journal of Theoretical Biology, vol.8, issue.2, pp.357-366, 1965.
DOI : 10.1016/0022-5193(65)90083-4

W. Maddison, Gene Trees in Species Trees, Systematic Biology, vol.46, issue.3, pp.523-536, 1998.
DOI : 10.1093/sysbio/46.3.523

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

J. Doyon, V. Ranwez, V. Daubin, and V. Berry, Models, algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol.12, issue.5, pp.392-400, 2011.
DOI : 10.1093/bib/bbr045
URL : https://hal.archives-ouvertes.fr/lirmm-00825041

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
DOI : 10.1073/pnas.1202997109

D. Sankoff and N. El-mabrouk, Duplication, rearrangement and reconciliation In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map alignment and the Evolution of Gene Families, Computational Biology, vol.1, 2000.

S. Bérard, C. Gallien, B. Boussau, G. Szöll?si, V. Daubin et al., Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.28, issue.18, pp.382-388, 2012.
DOI : 10.1093/bioinformatics/bts374

G. Szöll?si, E. Tannier, N. Lartillot, and V. Daubin, Lateral Gene Transfer from the Dead, Systematic Biology, vol.62, issue.3, pp.386-397, 2013.
DOI : 10.1093/sysbio/syt003

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

G. Szöll?si, W. Rosikiewicz, B. Bousseau, E. Tannier, and V. Daubin, Efficient Exploration of the Space of Reconciled Gene Trees, Systematic Biology, vol.62, issue.6, 2013.
DOI : 10.1093/sysbio/syt054

D. Sankoff, Minimal Mutation Trees of Sequences, SIAM Journal on Applied Mathematics, vol.28, issue.1, p.35, 1975.
DOI : 10.1137/0128004

. Patterson, 1186/1471-2105-14-S15-S4 Cite this article as Lateral gene transfer, rearrangement, reconciliation, BMC Bioinformatics, pp.10-14, 2013.