C. Barton, C. S. Iliopoulos, R. Kundu, S. P. Pissis, A. Retha et al., Accurate and Efficient Methods to Improve Multiple Circular Sequence Alignment, 14th SEA, pp.247-258, 2015.
DOI : 10.1007/978-3-319-20086-6_19

D. A. Benson, I. Karsch-mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp et al., GenBank, Nucleic Acids Research, vol.28, issue.1, pp.15-18, 2000.
DOI : 10.1093/nar/28.1.15

URL : http://doi.org/10.1093/nar/gkq1079

N. Bray and L. Pachter, MAVID: Constrained Ancestral Alignment of Multiple Sequences, Genome Research, vol.14, issue.4, pp.693-699, 2004.
DOI : 10.1101/gr.1960404

R. Brodie, A. J. Smith, R. L. Roper, V. Tcherepanov, and C. Upton, Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, vol.5, issue.1, p.96, 2004.
DOI : 10.1186/1471-2105-5-96

H. Bunke and U. Buhler, Applications of approximate string matching to 2D shape recognition, Pattern Recognition, vol.26, issue.12, pp.1797-1812, 1993.
DOI : 10.1016/0031-3203(93)90177-X

P. Burcsi, F. Cicalese, G. Fici, and Z. Lipták, ALGORITHMS FOR JUMBLED PATTERN MATCHING IN STRINGS, International Journal of Foundations of Computer Science, vol.81, issue.02, pp.357-374, 2012.
DOI : 10.1017/CBO9781107341005

S. Burkhardt, A. Crauser, P. Ferragina, H. P. Lenhof, E. Rivals et al., qgram based database searching using a suffix array (QUASAR), pp.3-77, 1999.
DOI : 10.1145/299432.299460

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

K. M. Chao, J. Zhang, J. Ostell, and W. Miller, A tool for aligning very similar DNA sequences, Bioinformatics, vol.13, issue.1, pp.75-80, 1997.
DOI : 10.1093/bioinformatics/13.1.75

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

S. Cohen, A. Houben, and D. Segal, Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants, The Plant Journal, vol.27, issue.6, pp.1027-1034, 2008.
DOI : 10.1111/j.1365-313X.2007.03394.x

D. J. Craik and N. M. Allewell, Thematic Minireview Series on Circular Proteins, Journal of Biological Chemistry, vol.287, issue.32, pp.26999-27000, 2012.
DOI : 10.1074/jbc.R112.390344

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411035

M. Crochemore, C. Hancart, and T. Lecroq, Algorithms on Strings, 2007.
DOI : 10.1017/CBO9780511546853

URL : https://hal.archives-ouvertes.fr/hal-00470109

D. Castillo, C. S. Hikima, J. I. Jang, H. B. Nho, S. W. Jung et al., Comparative Sequence Analysis of a Multidrug-Resistant Plasmid from Aeromonas hydrophila, Antimicrobial Agents and Chemotherapy, vol.57, issue.1, pp.120-129, 2013.
DOI : 10.1128/AAC.01239-12

T. Ehlers, F. Manea, R. Merca¸smerca¸s, and D. Nowotka, k-abelian pattern matching, 18th DLT, pp.178-190, 2014.
DOI : 10.1007/978-3-319-09698-8_16

F. Fernandes, L. Pereira, and A. T. Freitas, CSA: An efficient algorithm to improve circular DNA multiple alignment, BMC Bioinformatics, vol.10, issue.1, pp.1-13, 2009.
DOI : 10.1186/1471-2105-10-230

URL : http://doi.org/10.1186/1471-2105-10-230

J. Fischer, Inducing the LCP-Array, 12th WADS, pp.374-385, 2011.
DOI : 10.1007/978-3-642-22300-6_32

W. Fletcher and Z. Yang, INDELible: A Flexible Simulator of Biological Sequence Evolution, Molecular Biology and Evolution, vol.26, issue.8, pp.1879-1888, 2009.
DOI : 10.1093/molbev/msp098

A. Goios, L. Pereira, M. Bogue, V. Macaulay, and A. Amorim, mtDNA phylogeny and evolution of laboratory mouse strains, Genome Research, vol.17, issue.3, pp.293-298, 2007.
DOI : 10.1101/gr.5941007

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800920

O. Gotoh, An improved algorithm for matching biological sequences, Journal of Molecular Biology, vol.162, issue.3, pp.705-708, 1982.
DOI : 10.1016/0022-2836(82)90398-9

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

D. R. Helinski and D. B. Clewell, Circular DNA, Annual Review of Biochemistry, vol.40, issue.1, pp.899-942, 1971.
DOI : 10.1146/annurev.bi.40.070171.004343

T. Lee, J. C. Na, H. Park, K. Park, and J. S. Sim, Finding consensus and optimal alignment of circular strings, Theoretical Computer Science, vol.468, pp.92-101, 2013.
DOI : 10.1016/j.tcs.2012.11.018

URL : http://dx.doi.org/10.1016/j.tcs.2012.11.018

M. Maes, On a cyclic string-to-string correction problem, Information Processing Letters, vol.35, issue.2, pp.73-78, 1990.
DOI : 10.1016/0020-0190(90)90109-B

U. Manber and E. W. Myers, Suffix Arrays: A New Method for On-Line String Searches, SIAM Journal on Computing, vol.22, issue.5, pp.935-948, 1993.
DOI : 10.1137/0222058

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

A. Marzal and S. Barrachina, Speeding up the computation of the edit distance for cyclic strings, Proceedings 15th International Conference on Pattern Recognition. ICPR-2000, pp.891-894, 2000.
DOI : 10.1109/ICPR.2000.906217

A. Mosig, I. L. Hofacker, and P. F. Stadler, Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs, In: GCB. LNI, vol.83, pp.93-102, 2006.

S. B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-453, 1970.
DOI : 10.1016/0022-2836(70)90057-4

P. Peterlongo, G. T. Sacomoto, A. P. Do-lago, N. Pisanti, and M. F. Sagot, Lossless filter for multiple repeats with bounded edit distance, Algorithms for Molecular Biology, vol.4, issue.1, 2009.
DOI : 10.1186/1748-7188-4-3

URL : https://hal.archives-ouvertes.fr/hal-00784457

P. Peterlongo, N. Pisanti, F. Boyer, A. P. Do-lago, and M. F. Sagot, Lossless filter for multiple repetitions with Hamming distance, Journal of Discrete Algorithms, vol.6, issue.3, pp.497-509, 2008.
DOI : 10.1016/j.jda.2007.03.003

URL : https://hal.archives-ouvertes.fr/inria-00179731

N. Pisanti, M. Giraud, and P. Peterlongo, Filters and Seeds Approaches for Fast Homology Searches in Large Datasets, Algorithms in computational molecular biology, pp.299-320, 2010.
DOI : 10.1002/9780470892107.ch15

URL : https://hal.archives-ouvertes.fr/inria-00425370

C. P. Ponting and R. B. Russell, Swaposins: circular permutations within genes encoding saposin homologues, Trends in Biochemical Sciences, vol.20, issue.5, pp.179-180, 1995.
DOI : 10.1016/S0968-0004(00)89003-9

K. Rasmussen, J. Stoye, and E. Myers, -Matches over a Given Length, Journal of Computational Biology, vol.13, issue.2, pp.296-308, 2006.
DOI : 10.1089/cmb.2006.13.296

URL : https://hal.archives-ouvertes.fr/hal-00307305

P. Rice, I. Longden, and A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends in Genetics, vol.16, issue.6, pp.276-277, 2000.
DOI : 10.1016/S0168-9525(00)02024-2

E. Ukkonen, Approximate string-matching with q-grams and maximal matches, Theoretical Computer Science, vol.92, issue.1, pp.191-211, 1992.
DOI : 10.1016/0304-3975(92)90143-4

URL : http://doi.org/10.1016/0304-3975(92)90143-4

Z. Wang and M. Wu, Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite, PLoS ONE, vol.55, issue.10, p.110685, 2014.
DOI : 10.1371/journal.pone.0110685.s004

URL : http://doi.org/10.1371/journal.pone.0110685

J. Weiner and E. Bornberg-bauer, Evolution of Circular Permutations in Multidomain Proteins, Molecular Biology and Evolution, vol.23, issue.4, pp.734-743, 2006.
DOI : 10.1093/molbev/msj091