G. Blin, C. Chauve, and G. Fertin, The breakpoint distance for signed sequences, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00620356

D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B. Lang et al., Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome., Proceedings of the National Academy of Sciences, vol.89, issue.14, pp.6575-6579, 1992.
DOI : 10.1073/pnas.89.14.6575

G. Bourque, E. Zdobnov, P. Bork, P. Pevzner, and G. Tesler, Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages, Genome Research, vol.15, issue.1, pp.98-110, 2005.
DOI : 10.1101/gr.3002305

D. Sankoff, Gene and genome duplication, Current Opinion in Genetics & Development, vol.11, issue.6, pp.681-684, 2001.
DOI : 10.1016/S0959-437X(00)00253-7

J. Korbel, D. Snel, M. Huynen, and P. Bork, SHOT: a web server for the construction of genome phylogenies, Trends in Genetics, vol.18, issue.3, pp.158-162, 2002.
DOI : 10.1016/S0168-9525(01)02597-5

E. Belda, A. Moya, and F. Silva, Genome Rearrangement Distances and Gene Order Phylogeny in ??-Proteobacteria, Molecular Biology and Evolution, vol.22, issue.6, pp.1456-1467, 2005.
DOI : 10.1093/molbev/msi134

G. Blin, A. Chateau, C. Chauve, and Y. Gingras, Inferring Positional Homologs with Common Intervals of Sequences, Comparative Genomics, RECOMB 2006 International Workshop, pp.24-38, 2006.
DOI : 10.1007/11864127_3

URL : https://hal.archives-ouvertes.fr/hal-00620367

D. Bryant, The complexity of calculating exemplar distances, " in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, Kluwer Acad. Pub, pp.207-212, 2000.

X. Chen, J. Zheng, Z. Fu, P. Nan, Y. Zhong et al., COMPUTING THE ASSIGNMENT OF ORTHOLOGOUS GENES VIA GENOME REARRANGEMENT, Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, pp.302-315, 2005.
DOI : 10.1142/9781860947322_0037

K. Swenson, M. Marron, J. Earnest-deyoung, and B. Moret, Approximating the true evolutionary distance between two genomes, Proceedings of the Seventh Workshop on Algorithm Engineering and Experiments and the Second Workshop on Analytic Algorithmics and Combinatorics (ALENEX/ANALCO, pp.121-129, 2005.
DOI : 10.1145/1227161.1402297

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.154.556

N. C. Thach, Algorithms for calculating exemplar distances, 2005.

Z. Chen, B. Fu, and B. Zhu, The Approximability of the Exemplar Breakpoint Distance Problem, Algorithmic Aspects in Information and Management, Second International Conference, pp.291-302, 2006.
DOI : 10.1007/11775096_27

M. Marron, K. Swenson, and B. Moret, Genomic Distances under Deletions and Insertions, Theoretical Computer Science, vol.325, issue.3, pp.347-360, 2004.
DOI : 10.1016/j.tcs.2004.02.039

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.57.8269

J. Tang and B. Moret, Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content, Algorithms and Data Structures, pp.37-46, 2003.
DOI : 10.1007/978-3-540-45078-8_4

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.123.9677

Z. Fu, X. Chen, V. Vacic, P. Nan, Y. Zhong et al., A Parsimony Approach to Genome-Wide Ortholog Assignment, Research in Computational Molecular Biology, 10th Annual International Conference, pp.578-594, 2006.
DOI : 10.1007/11732990_47

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.91.128

C. Nguyen, Y. Tay, and L. Zhang, Divide-and-conquer approach for the exemplar breakpoint distance, Bioinformatics, vol.21, issue.10, pp.2171-2176, 2005.
DOI : 10.1093/bioinformatics/bti327

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.601.596

G. Blin and R. Rizzi, Conserved Interval Distance Computation Between Non-trivial Genomes, Computing and Combinatorics, 11th Annual International Conference, pp.22-31, 2005.
DOI : 10.1007/11533719_5

URL : https://hal.archives-ouvertes.fr/hal-00620353

G. Bourque, Y. Yacef, and N. El-mabrouk, Maximizing Synteny Blocks to Identify Ancestral Homologs, Comparative Genomics, RECOMB 2005 International Workshop, pp.21-34, 2005.
DOI : 10.1007/11554714_3

Z. Chen, R. Fowler, B. Fu, and B. Zhu, Lower Bounds on the Approximation of the Exemplar Conserved Interval Distance Problem of Genomes, Computing and Combinatorics, 12th Annual International Conference, pp.245-254, 2006.
DOI : 10.1007/11809678_27

S. Angibaud, G. Fertin, and I. Rusu, On the inapproximability of similarity measures between genomes containing duplicates, Preparation, 2006.

D. Sankoff and L. Haque, Power Boosts for Cluster Tests, Comparative Genomics, RECOMB 2005 International Workshop, pp.121-130, 2005.
DOI : 10.1007/11554714_11

A. Bergeron and J. Stoye, On the Similarity of Sets of Permutations and Its Applications to Genome Comparison, Computing and Combinatorics, 9th Annual International Conference, pp.68-79, 2003.
DOI : 10.1007/3-540-45071-8_9

M. Garey and D. Johnson, Computers and Intractability: a guide to the theory of NP-completeness, 1979.

C. H. Papadimitriou and M. Yannakakis, Optimization, approximation, and complexity classes, Journal of Computer and System Sciences, vol.43, issue.3, pp.425-440, 1991.
DOI : 10.1016/0022-0000(91)90023-X

URL : http://doi.org/10.1016/0022-0000(91)90023-x

U. Feige, A threshold of ln n for approximating set cover, Journal of the ACM, vol.45, issue.4, pp.634-652, 1998.
DOI : 10.1145/285055.285059

S. Eidenbenz, C. Stamm, and P. Widmayer, Positioning Guards at Fixed Height Above a Terrain ??? An Optimum Inapproximability Result, 6th European Symposiumal on Algorithms, pp.187-198, 1998.
DOI : 10.1007/3-540-68530-8_16

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.39.2349

S. Angibaud, G. Fertin, I. Rusu, and S. Vialette, How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation, Comparative Genomics, RECOMB 2006 International Workshop, pp.75-86, 2006.
DOI : 10.1007/11864127_7

URL : https://hal.archives-ouvertes.fr/hal-00619848

G. Guillaume-fertin, Fertin is a professor at LINA (Laboratoire d'Informatique de Nantes-Atlantique), University of Nantes, France. He completed his PhD degree from University His current interests of research are optimization, discrete mathematics, computational complexity and algorithms dedicated to bioinformatics, 1999.