B. Bauslaugh and F. Ruskey, Generating alternating permutations lexicographically, BIT, vol.8, issue.1, pp.17-26, 1990.
DOI : 10.1007/BF01932127
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.5084

S. Bérard, A. Bergeron, C. Chauve, and C. Paul, Perfect Sorting by Reversals Is Not Always Difficult, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.1, pp.4-16, 2007.
DOI : 10.1109/TCBB.2007.1011

J. R. Bitner, G. Ehrlich, and E. M. Reingold, Efficient generation of the binary reflected gray code and its applications, Communications of the ACM, vol.19, issue.9, pp.517-521, 1976.
DOI : 10.1145/360336.360343

M. Bouvel and E. Pergola, Posets and permutations in the duplicationloss model, Pure Math. Appl, vol.19, pp.2-3, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00322737

M. Bouvel and D. , Rossin, A variant of the tandem duplication-random loss model of genome rearrangement, Theoretical Computer Science, vol.410, pp.8-10, 2009.

E. R. Canfield and H. S. Wilf, Counting permutations by their alternating runs, Journal of Combinatorial Theory, Series A, vol.115, issue.2, pp.213-225, 2008.
DOI : 10.1016/j.jcta.2007.05.006
URL : http://doi.org/10.1016/j.jcta.2007.05.006

K. Chaudhuri, K. Chen, R. Mihaescu, and S. Rao, On the tandem duplication-random loss model of genome rearrangement, Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm , SODA '06, pp.564-570, 2006.
DOI : 10.1145/1109557.1109619

H. D. Chen, W. L. Fan, S. G. Kong, H. Lee, B. Zheng et al., Inverse symmetry in genomes and whole-genome inverse duplication, International Bioinformatics Workshop (IBW2008), 2008.

M. C. Chen and R. C. Lee, Sorting by transpositions based on the first increasing substring concept, Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering, p.553, 2004.

M. T. Hallett and J. Lagergren, New algorithms for the duplication-loss model, Proceedings of the fourth annual international conference on Computational molecular biology , RECOMB '00, pp.138-146, 2000.
DOI : 10.1145/332306.332359

S. Kitaev, Introduction to partially ordered patterns, Discrete Applied Mathematics, vol.155, issue.8, pp.929-944, 2007.
DOI : 10.1016/j.dam.2006.09.011
URL : http://doi.org/10.1016/j.dam.2006.09.011

S. Kitaev and A. Pyatkin, On avoidance of V -and ?-patterns in permutations, Ars Combinatoria, 2010.

A. Labarre, New Bounds and Tractable Instances for the Transposition Distance, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.3, issue.4, pp.380-394, 2006.
DOI : 10.1109/TCBB.2006.56
URL : https://hal.archives-ouvertes.fr/hal-00728947

R. Nussinov, Some indications for inverse DNA duplication, Journal of Theoretical Biology, vol.95, issue.4, p.783, 1982.
DOI : 10.1016/0022-5193(82)90353-8

R. Rieper and M. Zeleke, Valleyless sequences, ArXiv:math/0005180, 2000.

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

L. W. Shapiro, W. Woan, and S. Getu, Runs, Slides and Moments, SIAM Journal on Algebraic Discrete Methods, vol.4, issue.4, 1983.
DOI : 10.1137/0604046

N. J. Sloane, The On-Line Encyclopedia of Integer Sequences
DOI : 10.1007/978-3-540-73086-6_12

G. Blin, M. Crochemore, S. Hamel, and S. Vialette, Finding the median of three permutations under the Kendall-? distance, in: Permutation Patterns, Firenze, pp.13-17, 2009.

S. Effler and F. Ruskey, A CAT algorithm for generating permutations with a fixed number of inversions, Information Processing Letters, vol.86, issue.2, pp.107-112, 2003.
DOI : 10.1016/S0020-0190(02)00481-7

J. Joichi, D. E. White, and S. G. Williamson, Combinatorial Gray Codes, SIAM Journal on Computing, vol.9, issue.1, pp.130-141, 1980.
DOI : 10.1137/0209013

S. M. Johnson, Generation of permutations by adjacent transposition, Mathematics of Computation, vol.17, issue.83, pp.282-285, 1963.
DOI : 10.1090/S0025-5718-1963-0159764-2

P. Klingsberg, A Gray code for compositions, Journal of Algorithms, vol.3, issue.1, pp.41-44, 1981.
DOI : 10.1016/0196-6774(82)90006-2

D. E. Knuth, The Art of Computer Programming, 1997.

H. Steinhaus, One Hundred Problems in Elementary Mathematics, 1979.

H. F. Trotter, Algorithm 115: Perm, Communications of the ACM, vol.5, issue.8, pp.434-435, 1962.
DOI : 10.1145/368637.368660

V. Vajnovszki and T. Walsh, A loop-free two-close Gray-code algorithm for listing k-ary Dyck words, Journal of Discrete Algorithms, vol.4, issue.4, pp.633-648, 2006.
DOI : 10.1016/j.jda.2005.07.003

T. Walsh, Loop-free sequencing of bounded integer compositions, J. Combin. Math. Combin. Comput, vol.33, pp.323-345, 2000.

T. Walsh, Generating Gray Codes in O(1) Worst-Case Time per Word, LNCS, vol.2731, pp.7-12, 2003.
DOI : 10.1007/3-540-45066-1_5

H. S. Wilf, Combinatorial Algorithms: An Update, 1989.
DOI : 10.1137/1.9781611970166

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

E. Babson, Steingrimsson : « Generalized permutation patterns and a classification of the Mahonian statistics, Séminaire Lotharingien de Combinatoire, p.18, 2000.

S. Bacchelli, E. Barcucci, E. Grazzini, and E. , Pergola : « Exhaustive generation of combinatorial objects by ECO, Acta Informatica, vol.40, issue.8, pp.585-602, 2004.

E. Barcucci and A. Bernini, Poneti : « From Fibonacci to Catalan permutations ». arXiv, math/0612277v1, déc, 2006.

E. Barcucci, A. Del-lungo, E. Pergola, and R. Pinzani, ECO:a methodology for the enumeration of combinatorial objects, Journal of Difference Equations and Applications, vol.132, issue.3, pp.435-490, 1999.
DOI : 10.1016/0012-365X(94)00067-1

E. Barcucci, A. Del-lungo, and R. Pinzani, ???Deco??? polyominoes, permutations and random generation, Theoretical Computer Science, vol.159, issue.1, pp.29-42, 1996.
DOI : 10.1016/0304-3975(95)00199-9

J. Baril, Gray code for permutations with a fixed number of cycles, Discrete Mathematics, vol.307, issue.13, pp.1559-1571, 2007.
DOI : 10.1016/j.disc.2006.09.007

J. Baril, « Gray code for permutations with a fixed number of left-to-right minima », Ars Combinatoria, 2011.

J. Baril and V. , Gray code for derangements, Discrete Applied Mathematics, vol.140, issue.1-3, pp.207-221, 2004.
DOI : 10.1016/j.dam.2003.06.002

J. Baril and R. Vernay, Whole mirror duplication-random loss model and pattern avoiding permutations, Pattern Permutations 2009 Dipartimento Sistemi e Informatica, 2009.
DOI : 10.1016/j.ipl.2010.04.016
URL : https://hal.archives-ouvertes.fr/hal-00785281

J. Baril and R. Vernay, Whole mirror duplication-random loss model and pattern avoiding permutations, Information Processing Letters, vol.110, issue.11, pp.474-480, 2010.
DOI : 10.1016/j.ipl.2010.04.016
URL : https://hal.archives-ouvertes.fr/hal-00785281

B. Bauslaugh, Generating alternating permutations lexicographically, BIT, vol.8, issue.1, pp.17-26, 1990.
DOI : 10.1007/BF01932127

A. Bergeron and J. Mixtacki, A Unifying View of Genome Rearrangements, Algorithms in Bioinformatics, vol.4175, pp.163-173, 2006.
DOI : 10.1007/11851561_16

A. Bernini, E. Grazzini, and E. Pergola, A general exhaustive generation algorithm for Gray structures, Acta Informatica, vol.157, issue.1, pp.361-376, 2007.
DOI : 10.1007/s00236-007-0053-0

J. R. Bitner, G. Ehrlich, and E. M. , Efficient generation of the binary reflected gray code and its applications, Communications of the ACM, vol.19, issue.9, pp.517-521, 1976.
DOI : 10.1145/360336.360343

G. Blin, M. Crochemore, and S. Hamel, Vialette : « Finding the median of three permutations under de Kendall-? distance ». Pattern Permutations, pp.31-36, 2009.

G. Bourque and P. Pevzner, « Genome-scale evolution: reconstructing gene orders in the ancestral species », Genome Research, vol.12, issue.1, p.26, 2002.

M. Bouvel, Pergola : « Posets and Permutations in the duplication-loss model, Pure Math. Appl, vol.19, issue.2-3, pp.71-80, 2008.

M. Bouvel, Pergola : « Posets and permutations in the duplication-loss model: minimal permutations with d descents, Theoretical Computer Science, vol.411, pp.26-282487, 2010.

M. Bouvel, A variant of the tandem duplication ??? random loss model of genome rearrangement, Theoretical Computer Science, vol.410, issue.8-10, pp.847-858, 2009.
DOI : 10.1016/j.tcs.2008.11.017
URL : https://hal.archives-ouvertes.fr/hal-00206178

S. Bérard, A. Bergeron, C. Chauve, and C. , Perfect Sorting by Reversals Is Not Always Difficult, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.1, pp.4-16, 2007.
DOI : 10.1109/TCBB.2007.1011

S. Bérard, C. Chauve, and C. , Paul : « A more efficient algorithm for perfect sorting by reversals ». Information processing letters, pp.90-95, 2008.

E. R. Canfield and H. , Wilf : « Counting permutations by their alternating runs », Journal of Combinatorial Theory, issue.115, pp.213-225, 2008.

C. C. Chang, C. Y. Chen, and H. Y. , Symbolic Gray Code As A Data Allocation Scheme For Two-disc Systems, The Computer Journal, vol.35, issue.3, p.299, 1992.
DOI : 10.1093/comjnl/35.3.299

C. C. Chang, M. W. Du, and R. C. , Lee : « Symbolic Gray code as a perfect multiattribute hashing scheme for partial match queries ». Software Engineering, IEEE Transactions on, vol.8, issue.3, pp.235-249, 1982.

K. Chaudhuri, K. Chen, R. Mihaescu, and S. Rao, « On the tandem duplicationrandom loss model of genome rearrangement, Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm, pp.564-570, 2006.

H. D. Chen, W. L. Fan, S. G. Kong, H. Lee, B. Zheng et al., Inverse symmetry in genomes and whole-genome inverse duplication, International Bioinformatics Workshop (IBW2008). Yunnan University, 2008.

M. C. Chen and R. C. , Lee : « Sorting by transpositions based on the first increasing substring concept, BIBE, p. 553, 2004.

M. Cohn and J. P. , Robinson : « Counting sequences, IEEE Transactions on Computers, vol.30, issue.1, pp.17-23, 1981.

G. R. Crabtree, A. J. Fornace, J. A. Kant, O. W. Mcbride, D. Saxe et al., Simon : « Evolution and organization of the fibrinogen locus on chromosome 4: gene duplication accompanied by transposition and inversion, National Academy of Sciences of the United States of America, p.2344, 1985.

M. Dukes, M. Flanagan, and T. Mansour, Vajnovszki : « Combinatorial Gray codes for classes of pattern avoiding permutations, Theoretical Computer Science, issue.396, pp.35-49, 2008.

S. Effler and F. , Ruskey : « A CAT algorithm for generating permutations with a fixed number of inversions », Information Processing Letters, issue.86, pp.107-112, 2003.

P. Flajolet, A Note on Gray Code and Odd-Even Merge, SIAM Journal on Computing, vol.9, issue.1, p.142, 1980.
DOI : 10.1137/0209014

D. Foata, On the Netto inversion number of a sequence, Proceedings of the, pp.236-240, 1968.
DOI : 10.1090/S0002-9939-1968-0223256-9

D. Foata and M. P. , Major Index and Inversion Number of Permutations, Mathematische Nachrichten, vol.20, issue.1, pp.143-159, 1978.
DOI : 10.1002/mana.19780830111

M. Gardner, Mathematical Games, Scientific American, vol.227, issue.2, pp.106-109, 1972.
DOI : 10.1038/scientificamerican0872-106

S. Getu, L. W. Shapiro, and W. J. , Woan : « Runs, slides and moments », SIAM Journal on Algebraic and Discrete Methods, vol.4, p.459, 1983.

E. Gilbert, Gray Codes and Paths on the n-Cube, Bell System Technical Journal, vol.37, issue.3, pp.815-826, 1958.
DOI : 10.1002/j.1538-7305.1958.tb03887.x

H. W. Gould, « The q-Stirling numbers of first and second kinds ». Duke mathematical journal, pp.281-289, 1961.

O. Guibert, Combinatoire des permutations à motifs exclus en liaison avec mots, cartes planaires et tableaux de Young, Thèse de doctorat, 1995.

M. T. Hallett and J. , Lagergren : « New algorithms for the duplication-loss model, Proceedings of the fourth annual international conference on Computational molecular biology, pp.138-146, 2000.

F. Heath, Origins of the Binary Code, Origins of the binary code, pp.76-83, 1972.
DOI : 10.1038/scientificamerican0872-76

S. M. Johnson, Generation of permutations by adjacent transposition, Mathematics of Computation, vol.17, issue.83, pp.282-285, 1962.
DOI : 10.1090/S0025-5718-1963-0159764-2

J. T. Joichi, D. White, and S. G. Williamson, Combinatorial Gray Codes, Combinatorial gray codes, pp.130-141, 1980.
DOI : 10.1137/0209013

S. Kitaev, Introduction to partially ordered patterns, Discrete Applied Mathematics, vol.155, issue.8, pp.929-944, 2007.
DOI : 10.1016/j.dam.2006.09.011
URL : http://doi.org/10.1016/j.dam.2006.09.011

S. Kitaev, Pyatkin : « On avoidance of V-and A-patterns in permutations ». oct, 2006.

P. Klingsberg, A Gray code for compositions, Journal of Algorithms, vol.3, issue.1, pp.41-44, 1981.
DOI : 10.1016/0196-6774(82)90006-2

D. Knuth, Sorting and searching ». The art of computer programming, 1982.

D. Knuth, « Generating all combinations and partitions ». The art of computer programming, 2005.

D. Knuth, « Generating all tuples and permutations ». The art of computer programming, 2005.

A. Labarre, A New Tight Upper Bound on the Transposition Distance, Algorithms in Bioinformatics 5th International Workshop WABI 2005, pp.216-227, 2005.
DOI : 10.1007/11557067_18
URL : https://hal.archives-ouvertes.fr/hal-00728796

J. M. Lucas, F. Ruskey, and D. R. Van-baronaigien, On Rotations and the Generation of Binary Trees, Journal of Algorithms, vol.15, issue.3, pp.343-366, 1993.
DOI : 10.1006/jagm.1993.1045

P. A. Mac-mahon, The Indices of Permutations and the Derivation Therefrom of Functions of a Single Variable Associated with the Permutations of any Assemblage of Objects, American Journal of Mathematics, vol.35, issue.3, pp.281-322, 1913.
DOI : 10.2307/2370312

T. Mansour and S. Yan, Minimal permutations with <mml:math altimg="si10.gif" display="inline" overflow="scroll" xmlns:xocs="http://www.elsevier.com/xml/xocs/dtd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.elsevier.com/xml/ja/dtd" xmlns:ja="http://www.elsevier.com/xml/ja/dtd" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:tb="http://www.elsevier.com/xml/common/table/dtd" xmlns:sb="http://www.elsevier.com/xml/common/struct-bib/dtd" xmlns:ce="http://www.elsevier.com/xml/common/dtd" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cals="http://www.elsevier.com/xml/common/cals/dtd"><mml:mi>d</mml:mi></mml:math> descents, Minimal permutations with d descents, pp.1445-1460, 2010.
DOI : 10.1016/j.ejc.2010.01.001

A. Nijenhuis and H. Wilf, [76] R. Nussinov : « Some indications for inverse DNA duplication », Combinatorial algorithms, p.783, 1978.

D. Richards, Data compression and gray-code sorting, Information Processing Letters, vol.22, issue.4, pp.201-205, 1986.
DOI : 10.1016/0020-0190(86)90029-3

F. Ruskey, -Ary Trees Lexicographically, SIAM Journal on Computing, vol.7, issue.4, p.424, 1978.
DOI : 10.1137/0207034
URL : https://hal.archives-ouvertes.fr/hal-01184798

F. Ruskey, Adjacent interchange generation of combinations, Journal of Algorithms, vol.9, issue.2, pp.162-180, 1988.
DOI : 10.1016/0196-6774(88)90036-3

D. Sankoff, Short inversions and conserved gene clusters, ACM symposium on Applied computing, pp.164-167, 2002.

C. Savage, « A survey of combinatorial Gray codes ». SIAM review, pp.605-629, 1997.

E. Steingrimsson, Statistics on ordered partitions of sets ». arXiv, ma- th/0605670, avr, 2007.

H. F. Trotter, Algorithm 115: Perm, Communications of the ACM, vol.5, issue.8, pp.434-435, 1962.
DOI : 10.1145/368637.368660

V. Vajnovszki, Generating a Gray code for p-sequences », Journal of Mathematical Modelling and Algorithms, vol.1, issue.1, pp.31-41, 2002.
DOI : 10.1023/A:1015622720041

V. Vajnovszki, Gray visiting Motzkins, Gray visiting motzkins, pp.793-811, 2002.
DOI : 10.1007/s00236-002-0097-0

V. Vajnovszki, Generating involutions, derangements, and relatives by ECO, Discrete Mathematics and Theoretical Computer Science, vol.12, issue.1, p.109, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00824068

V. Vajnovszki and R. , Vernay : « Restricted compositions and permutations: from old to new Gray codes, 8th French Combinatorial Conference, 2010.

V. Vajnovszki and R. , Restricted compositions and permutations: From old to new Gray codes, Information Processing Letters, vol.111, issue.13, pp.650-655, 2011.
DOI : 10.1016/j.ipl.2011.03.022

V. Vajnovszki and T. Walsh, A loop-free two-close Gray-code algorithm for listing k-ary Dyck words, Journal of Discrete Algorithms, vol.4, issue.4, pp.633-648, 2006.
DOI : 10.1016/j.jda.2005.07.003

M. Wachs, p, q-Stirling numbers and set partition statistics, Journal of Combinatorial Theory, Series A, vol.56, issue.1, pp.27-46, 1991.
DOI : 10.1016/0097-3165(91)90020-H

T. Walsh, Loop-free sequencing of bounded integer compositions », Journal of Combinatorial Mathematics and Combinatorial Computing, vol.33, pp.323-345, 2000.

T. Walsh, Generating Gray Codes in O(1) Worst-Case Time per Word, 4th international conference on Discrete mathematics and theoretical computer science, pp.73-88, 2003.
DOI : 10.1007/3-540-45066-1_5

J. West, Generating trees and the Catalan and Schröder numbers, Discrete Mathematics, vol.146, issue.13, pp.246-262, 1995.