J. Allali and M. Sagot, The at most k-deep factor tree, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00627813

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

M. Brudno, M. Chapman, B. Göttgens, S. Batzoglou, and B. , Morgenstern: Fast and sensitive multiple alignment of large genomic sequences, BMC Bioinformatics, vol.4, issue.1, p.66, 2003.
DOI : 10.1186/1471-2105-4-66

M. Brudno, C. B. Do, G. M. Cooper, M. Kim, E. Davydov et al., LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA, Genome Research, vol.13, issue.4, pp.721-731, 2003.
DOI : 10.1101/gr.926603

S. Burkhardt, A. Crauser, P. Ferragina, H. P. Lenhof, and M. , Vingron: q-gram based database searching using a suffix array (QUASAR), Proceedings of the third annual international conference on Computational molecular biology (Recomb 99), pp.77-83, 1999.

S. Burkhardt and J. Kärkkäinen, Better Filtering with Gapped q-Grams, Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching, pp.73-85, 2001.
DOI : 10.1007/3-540-48194-X_6

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.5942

S. Burkhardt and J. Kärkkäinen, One-Gapped q-Gram Filters for Levenshtein Distance, 13th Annual Symposium on Combinatorial Pattern Matching, pp.225-234, 2002.
DOI : 10.1007/3-540-45452-7_19

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

L. Gravano, P. Ipeirotis, H. Jagadish, N. Koudas, S. Muthukrishnan et al., Approximate string joins in a database (almost) for free, Proc. of 27th Int'l Conf. on Very Large DataBases, pp.491-500, 2001.

M. Höhl, S. Kurtz, and E. Ohlebusch, Efficient multiple genome alignment, Bioinformatics, vol.18, issue.Suppl 1, pp.312-320, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S312

J. Kärkkäinen, Computing the Threshold for q-Gram Filters, Proceedings of the 8th Scandinavian Workshop on Algorithm Theory, pp.348-357, 2002.
DOI : 10.1007/3-540-45471-3_36

G. Kucherov, L. Noe, and M. Roytberg, Multiseed Lossless Filtration, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.2, issue.1, pp.51-61, 2005.
DOI : 10.1109/TCBB.2005.12

URL : https://hal.archives-ouvertes.fr/inria-00354810

M. Li and B. Ma, PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH, Journal of Bioinformatics and Computational Biology, vol.02, issue.03, pp.164-175, 2003.
DOI : 10.1142/S0219720004000661

D. J. Lipman and W. R. Pearson, Rapid and sensitive protein similarity searches, Science, vol.227, issue.4693, pp.1435-1441, 1985.
DOI : 10.1126/science.2983426

B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440

L. Marsan and M. Sagot, Extracting structured motifs using a suffix tree -algorithms and application to promoter consensus identification, RECOMB, pp.210-219, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00427093

M. Michael, C. Dieterich, and M. Vingron, SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors, Bioinformatics, vol.21, issue.9, pp.2093-2094, 2005.
DOI : 10.1093/bioinformatics/bti224

J. Na, A. Apostolico, C. Iliopoulos, and K. Park, Truncated suffix trees and their application to data compression, Theoretical Computer Science, vol.304, issue.1-3, pp.87-101, 2003.
DOI : 10.1016/S0304-3975(03)00053-7

URL : http://doi.org/10.1016/s0304-3975(03)00053-7

J. Na and K. Park, Data compression with truncated suffix trees, Data Compression Conference, p.565, 2000.

G. Navarro, E. Sutinen, J. Tanninen, and J. Tarhio, Indexing text with approximate q-grams, 11th Annual Symposium on Combinatorial Pattern Matching, pp.350-363, 1848.

P. Peterlongo, N. Pisanti, F. Boyer, and M. , Sagot: Lossless filter for finding long multiple approximate repetitions using a new data structure, the bi-factor array, String Processing and Information Retrieval (SPIRE 2005), 3772 of LNCS 2005, pp.179-190

P. Pevzner and M. Waterman, Multiple filtration and approximate pattern matching, Algorithmica, vol.35, issue.10, pp.135-154, 1995.
DOI : 10.1007/BF01188584

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.78.4723

N. Pisanti, A. Carvalho, L. Marsan, and M. Sagot, RISOTTO: Fast Extraction of Motifs with Mismatches, Proceedings of the 7th Latin American Theoretical Informatics Symposium, pp.757-768, 2006.
DOI : 10.1007/11682462_69

URL : https://hal.archives-ouvertes.fr/hal-00428023

K. R. Rasmussen, J. Stoye, and E. W. Myers, Efficient q-gram filters for finding all ?matches over a given length, 9th Annual International Conference, pp.189-203, 2005.

E. Sutinen and J. Tarhio, On using q-gram locations in approximate string matching, Third Annual European Symposium, pp.327-340, 1995.
DOI : 10.1007/3-540-60313-1_153

P. Thébault, S. Degivry, T. Schiex, and C. Gaspin, Combining constraint processing and pattern matching to describe and locate structured motifs in genomic sequences, Fifth IJCAI- 05 Workshop on Modelling and Solving Problems with Constraints, pp.330-337, 2005.

E. Ukkonen, On-line construction of suffix-trees. Algorithmica, pp.249-260, 1995.