M. S. Bansal, E. J. Alm, and M. Kellis, Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss, Journal of Computational Biology, vol.20, issue.10, pp.738-754, 2013.
DOI : 10.1089/cmb.2013.0073

S. Bérard, C. Gallien, B. Boussau, G. J. Szöllosi, V. Daubin et al., Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.28, issue.18, pp.28382-388, 2012.
DOI : 10.1093/bioinformatics/bts374

P. Biller, P. Feijão, and J. Meidanis, Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.1, pp.122-134, 2013.
DOI : 10.1109/TCBB.2012.168

T. M. Chan, Optimal output-sensitive convex hull algorithms in two and three dimensions, Discrete & Computational Geometry, vol.6, issue.4, pp.361-368, 1996.
DOI : 10.1007/BF02712873

C. Chauve, N. El-mabrouk, L. Gueguen, M. Semeria, and E. Tannier, Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later, Models and Algorithms for Genome Evolution, pp.47-62, 2013.
DOI : 10.1007/978-1-4471-5298-9_4

C. Chauve, Y. Ponty, and J. P. Zanetti, Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach, BSB, pp.49-56, 2014.
DOI : 10.1007/978-3-319-12418-6_7

URL : https://hal.archives-ouvertes.fr/hal-01216782

Y. Gagnon, M. Blanchette, and N. El-mabrouk, A flexible ancestral genome reconstruction method based on gapped adjacencies, BMC Bioinformatics, pp.13-19, 2012.

D. Gusfield, K. Balasubramanian, and D. Naor, Parametric optimization of sequence alignment, Algorithmica, vol.89, issue.3, pp.312-326, 1994.
DOI : 10.1007/BF01185430

M. W. Hahn, Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution, Genome Biology, vol.8, issue.7, p.141, 2007.
DOI : 10.1186/gb-2007-8-7-r141

R. Libeskind-hadas, Y. Wu, M. S. Bansal, and M. Kellis, Pareto-optimal phylogenetic tree reconciliation, Bioinformatics, vol.30, issue.12, pp.87-95, 2014.
DOI : 10.1093/bioinformatics/btu289

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058917

J. Ma, A. Ratan, B. J. Raney, B. B. Suh, L. Zhang et al., 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

J. Manuch, M. Patterson, R. Wittler, C. Chauve, and E. Tannier, Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, pp.13-19, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00773071

L. Pachter and B. Sturmfels, Parametric inference for biological sequence analysis, Proceedings of the National Academy of Sciences, vol.101, issue.46, pp.16138-16143, 2004.
DOI : 10.1073/pnas.0406011101

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528961

L. Pachter and B. Sturmfels, Tropical geometry of statistical models, Proceedings of the National Academy of Sciences, vol.101, issue.46, pp.16132-16137, 2004.
DOI : 10.1073/pnas.0406010101

C. Saule and R. Giegerich, Observations on the feasibility of exact Pareto optimization, Proceedings of CMSR 2014, pp.43-56, 2014.

T. Schnattinger, U. Schöning, and H. A. Kestler, Structural RNA alignment by multi-objective optimization, Bioinformatics, vol.29, issue.13, pp.1607-1613, 2013.
DOI : 10.1093/bioinformatics/btt188

E. Tannier, C. Zheng, and D. Sankoff, Multichromosomal median and halving problems under different genomic distances, BMC Bioinformatics, vol.10, issue.1, 2009.
DOI : 10.1186/1471-2105-10-120

URL : https://hal.archives-ouvertes.fr/hal-00428359