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
Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.28, issue.18, pp.28382-388, 2012. ,
DOI : 10.1093/bioinformatics/bts374
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
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
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
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
A flexible ancestral genome reconstruction method based on gapped adjacencies, BMC Bioinformatics, pp.13-19, 2012. ,
Parametric optimization of sequence alignment, Algorithmica, vol.89, issue.3, pp.312-326, 1994. ,
DOI : 10.1007/BF01185430
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
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
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
Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, pp.13-19, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00773071
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
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
Observations on the feasibility of exact Pareto optimization, Proceedings of CMSR 2014, pp.43-56, 2014. ,
Structural RNA alignment by multi-objective optimization, Bioinformatics, vol.29, issue.13, pp.1607-1613, 2013. ,
DOI : 10.1093/bioinformatics/btt188
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