M. Blanchette, T. Kunisawa, and D. Sankoff, Parametric genome rearrangement, Gene, vol.172, issue.1, pp.11-18, 1996.

C. Baudet, U. Dias, and Z. Dias, Sorting by weighted inversions considering length and symmetry, BMC Bioinform, vol.16, p.3, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01316998

P. Biller, C. Knibbe, L. Guéguen, and E. Tannier, Breaking good: accounting for the diversity of fragile regions for estimating rearrangement distances

, Genome Biol Evol, vol.8, pp.1427-1466, 2016.

J. H. Nadeau and B. A. Taylor, Lengths of chromosomal segments conserved since divergence of man and mouse, Proc Natl Acad Sci, vol.81, issue.3, pp.814-822, 1984.

S. Ohno, Evolution by gene duplication, p.160, 1970.

G. Fertin, G. Jean, and E. Tannier, Algorithms for computing the double cut and join distance on both gene order and intergenic sizes, Algorithms Mol Biol, vol.12, issue.1, p.16, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01533200

L. Bulteau, G. Fertin, and E. Tannier, Genome rearrangements with indels in intergenes restrict the scenario space, BMC Bioinform, vol.17, issue.14, p.426, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01396842

E. Lieberman-aiden, V. Berkum, N. L. Williams, L. Imakaev, M. Ragoczy et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, issue.5950, pp.289-93, 2009.

A. Veron, C. Lemaitre, C. Gautier, V. Lacroix, and M. Sagot, ):303. cost(i, j) = max(cost(i, s) + cost(s + 1, q) + cost(q, j) + ?(i, q)| i ? s < q ? j), BMC Genomics, vol.12, issue.1, 2011.

S. Pulicani, P. Simonaitis, E. Rivals, and K. M. Swenson, Rearrangement scenarios guided by chromatin structure, RECOMB international workshop on comparative genomics, pp.141-55, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01791974

K. M. Swenson, P. Simonaitis, and M. Blanchette, Models and algorithms for genome rearrangement with positional constraints, Algorithms Mol Biol, vol.11, issue.1, p.13, 2016.
URL : https://hal.archives-ouvertes.fr/lirmm-01348502

P. Simonaitis and K. M. Swenson, Finding local genome rearrangements, Algorithms Mol Biol, vol.13, issue.1, p.9, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-01794757

S. Yancopoulos, O. Attie, and R. Friedberg, Efficient sorting of genomic permutations by translocation, inversion and block interchange, Bioinformatics, vol.21, issue.16, pp.3340-3346, 2005.

A. Bergeron, J. Mixtacki, and J. Stoye, A unifying view of genome rearrangements, International workshop on algorithms in bioinformatics, pp.163-73, 2006.

M. Shao and Y. Lin, Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion, BMC Bioinform, vol.13, p.13, 2012.

B. K. Fosdick, D. B. Larremore, J. Nishimura, and J. Ugander, Configuring random graph models with fixed degree sequences, SIAM Rev, vol.60, issue.2, pp.315-55, 2018.

V. Bafna and P. A. Pevzner, Genome rearrangements and sorting by reversals, SIAM J Comput, vol.25, issue.2, pp.272-89, 1996.

A. Amir and A. Levy, String rearrangement metrics: a survey. Algorithms and applications, pp.1-33, 2010.

F. Farnoud and O. Milenkovic, Sorting of permutations by cost-constrained transpositions, IEEE Trans Inf Theory, vol.58, issue.1, pp.3-23, 2012.

D. Bienstock and O. Günlük, A degree sequence problem related to network design, Networks, vol.24, issue.4, pp.195-205, 1994.

T. Feder, A. Guetz, M. Mihail, and A. Saberi, A local switch markov chain on given degree graphs with application in connectivity of peer-to-peer networks, FOCS'06. 47th annual IEEE symposium on foundations of computer science, pp.69-76, 2006.

A. Caprara, Sorting by reversals is difficult, Proceedings of the first annual international conference on computational molecular biology, pp.75-83, 1997.

M. Braga, M. Sagot, C. Scornavacca, and E. Tannier, Bioinformatics research and applications: proceedings from ISBRA. The solution space of sorting by reversals, 2007.

J. R. Bitner, An asymptotically optimal algorithm for the dutch national flag problem, SIAM J Comput, vol.11, issue.2, pp.243-62, 1982.

M. Shao, Y. Lin, and B. Moret, Sorting genomes with rearrangements and segmental duplications through trajectory graphs, BMC Bioinform, vol.14, p.9, 2013.

E. Birmelé, R. Ferreira, R. Grossi, A. Marino, N. Pisanti et al., Optimal listing of cycles and st-paths in undirected graphs, Proceedings of the twenty-fourth annual ACM-SIAM symposium on discrete algorithms, pp.1884-96, 2013.

A. Caprara, A. Panconesi, and R. Rizzi, Packing cycles and cuts in undirected graphs, European symposium on algorithms, pp.512-535, 2001.

X. Zeng, M. J. Nesbitt, P. J. Wang, K. Vergara, I. A. Chen et al., Orthocluster: a new tool for mining synteny blocks and applications in comparative genomics, Proceedings of the 11th international conference on extending database technology: advances in database technology, pp.656-67, 2008.

N. Alexeev and M. A. Alekseyev, Estimation of the true evolutionary distance under the fragile breakage model, BMC Genomics, vol.18, issue.4, p.356, 2017.

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