E. Barghini, The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome, Genome Biology and Evolution, vol.6, issue.4, pp.776-91, 2014.
DOI : 10.1093/gbe/evu058

P. Novák, RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads, Bioinformatics, vol.29, issue.6, pp.79279-79282, 2013.
DOI : 10.1093/bioinformatics/btt054

K. Nakamura, Sequence-specific error profile of Illumina sequencers, Nucleic Acids Research, vol.39, issue.13, 2011.
DOI : 10.1093/nar/gkr344

C. Luo, Roche 454 sequencing technologies on the same microbial community DNA sample, Direct comparisons of Illumina vs, 2012.

J. Jurka, Repbase Update, a database of eukaryotic repetitive elements, Repbase Update, pp.462-467, 2005.
DOI : 10.1159/000084979

C. M. Bergman and . Et-quesneville, Discovering and detecting transposable elements in genome sequences, Briefings in Bioinformatics, vol.8, issue.6, pp.382-392, 2007.
DOI : 10.1093/bib/bbm048

S. Kurtz, A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes, BMC Genomics, vol.9, issue.1, p.517, 2008.
DOI : 10.1186/1471-2164-9-517

S. Kurtz, REPuter: the manifold applications of repeat analysis on a genomic scale, Nucleic Acids Research, vol.29, issue.22, pp.4633-4675, 2001.
DOI : 10.1093/nar/29.22.4633

N. Volfovsky, B. J. Et-haas, and S. L. Salzberg, A clustering method for repeat analysis in DNA sequences, Genome Biol, vol.8, issue.2, p.27, 2001.

A. Morgulis, WindowMasker: window-based masker for sequenced genomes, Bioinformatics, vol.22, issue.2, pp.134-175, 2006.
DOI : 10.1093/bioinformatics/bti774

G. Marcais and C. Et-kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, vol.27, issue.6, pp.764-770, 2011.
DOI : 10.1093/bioinformatics/btr011

W. Gu, Identification of repeat structure in large genomes using repeat probability clouds, Analytical Biochemistry, vol.380, issue.1, pp.77-83, 2008.
DOI : 10.1016/j.ab.2008.05.015

G. Achaz, Repseek, a tool to retrieve approximate repeats from large DNA sequences, Bioinformatics, vol.23, issue.1, pp.119-140, 2007.
DOI : 10.1093/bioinformatics/btl519

S. Kurtz and G. Et-myers, Estimating the probability of approximate matches, Lecture Notes in Computer Science, vol.1264, pp.52-64, 1997.
DOI : 10.1007/3-540-63220-4_49

D. R. Zerbino and E. Et-birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107

S. F. Altschul, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

R. C. Edgar and E. W. Et-myers, PILER: identification and classification of genomic repeats, Bioinformatics, vol.21, issue.Suppl 1, p.18, 2005.
DOI : 10.1093/bioinformatics/bti1003

J. Debarry, R. Liu, and . Et-bennetzen, Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm, BMC Bioinformatics, vol.9, issue.1, pp.235-245, 2008.
DOI : 10.1186/1471-2105-9-235

N. Blast-johnson and M. , NCBI BLAST: a better web interface, Nucleic Acids Research, vol.36, issue.Web Server, pp.5-9, 2008.
DOI : 10.1093/nar/gkn201

A. Schäffer, Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements, Nucleic Acids Research, vol.29, issue.14, pp.2994-3005, 2001.
DOI : 10.1093/nar/29.14.2994

A. Smit, R. Hubley, and P. Et-green, RepeatMasker Open-3.0. [En ligne] 1996-2010

R. C. Kennedy, An automated homology-based approach for identifying transposable elements, BMC Bioinformatics, vol.12, issue.1, p.130, 2011.
DOI : 10.1093/nar/gkn857

S. C. Robb, The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice, G3: Genes|Genomes|Genetics, vol.3, issue.6, pp.949-957, 2013.
DOI : 10.1534/g3.112.005348

Y. Han, J. M. Burnette, and . Wessler, TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences, Nucleic Acids Research, vol.37, issue.11, p.78, 2009.
DOI : 10.1093/nar/gkp295

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
URL : http://doi.org/10.1093/nar/gkh340

. Fasttree, Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

M. N. Price, P. S. Dehal, and A. P. Et-arkin, FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix, Molecular Biology and Evolution, vol.26, issue.7, pp.1641-1650, 2009.
DOI : 10.1093/molbev/msp077

X. Huang and A. Et-madan, CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-77, 1999.
DOI : 10.1101/gr.9.9.868

M. Bailly-bechet, A. Haudry, and E. Et-lerat, ???One code to find them all???: a perl tool to conveniently parse RepeatMasker output files, Mobile DNA, vol.5, issue.1, pp.10-1186, 2014.
DOI : 10.1016/j.tig.2007.02.006

T. M. Keane, K. Wong, and D. Et-adams, RetroSeq: transposable element discovery from next-generation sequencing data, Bioinformatics, vol.29, issue.3, pp.389-390, 2012.
DOI : 10.1093/bioinformatics/bts697
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562067

H. Web-server-finn, R. D. Clements, J. Eddy, and S. R. , HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.suppl, pp.29-37, 2011.
DOI : 10.1093/nar/gkr367

Y. Zhang and M. J. Et-zaki, SMOTIF: efficient structured pattern and profile motif search, Algorithms for Molecular Biology, vol.1, issue.1, p.22, 2006.
DOI : 10.1186/1748-7188-1-22

J. Nicolas, Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes, Bioinformatics, vol.21, issue.24, pp.4408-4418, 2005.
DOI : 10.1093/bioinformatics/bti710

T. Flutre, Considering Transposable Element Diversification in De Novo Annotation Approaches, PLoS ONE, vol.25, issue.3, p.16526, 2011.
DOI : 10.1371/journal.pone.0016526.s021
URL : https://hal.archives-ouvertes.fr/hal-00568705

. Triannot, A Versatile. ; High Performance Pipeline for the Automated Annotation of Plant Genomes

V. Singh and . Mishra, RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes, BMC Bioinformatics, vol.11, issue.1, pp.1471-2105, 1186.
DOI : 10.1186/1471-2105-11-609

E. M. Mccarthy and J. F. Et-mcdonald, LTR_STRUC: a novel search and identification program for LTR retrotransposons, Bioinformatics, vol.19, issue.3, pp.362-367, 2003.
DOI : 10.1093/bioinformatics/btf878

A. Kalyanaraman and S. Et-aluru, EFFICIENT ALGORITHMS AND SOFTWARE FOR DETECTION OF FULL-LENGTH LTR RETROTRANSPOSONS, Journal of Bioinformatics and Computational Biology, vol.04, issue.02, pp.197-216, 2006.
DOI : 10.1142/S021972000600203X

Z. Xu and H. Wang, LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Research, vol.35, issue.Web Server, pp.265-268, 2007.
DOI : 10.1093/nar/gkm286

M. Rho, De novo identification of LTR retrotransposons in eukaryotic genomes, BMC Genomics, vol.8, issue.1, p.90, 2007.
DOI : 10.1186/1471-2164-8-90

T. Kronmiller, B. A. Et-wise, and R. P. , TEnest: Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements, PLANT PHYSIOLOGY, vol.146, issue.1, pp.45-59, 2008.
DOI : 10.1104/pp.107.110353

A. L. Price, N. C. Jones, and P. Et-pevzner, De novo identification of repeat families in large genomes, Bioinformatics, vol.21, issue.Suppl 1, pp.351-359, 2005.
DOI : 10.1093/bioinformatics/bti1018

H. Quesneville, D. Nouaud, and . Et-anxolabéhère, Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes, Journal of Molecular Evolution, vol.57, issue.0, pp.50-59, 2003.
DOI : 10.1007/s00239-003-0007-2

X. Huang, On global sequence alignment, Bioinformatics, vol.10, issue.3, pp.227-235, 1994.
DOI : 10.1093/bioinformatics/10.3.227

K. Katoh and H. Et-toh, Recent developments in the MAFFT multiple sequence alignment program, Briefings in Bioinformatics, vol.9, issue.4, pp.286-298, 2008.
DOI : 10.1093/bib/bbn013

R. Kolpakov, G. Bana, and G. Et-kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acids Research, vol.31, issue.13, pp.3672-3678, 2003.
DOI : 10.1093/nar/gkg617
URL : https://hal.archives-ouvertes.fr/inria-00099597

L. Ellinghaus, D. Kurtz, S. Et-willhoeft, and U. , LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics, vol.9, issue.1, p.18, 2008.
DOI : 10.1186/1471-2105-9-18

G. Gremme, S. Steinbiss, and S. Et-kurtz, GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.3, pp.645-656, 2013.
DOI : 10.1109/TCBB.2013.68

M. Darzentas and N. , MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences, Bioinformatics, vol.26, issue.19, pp.2452-2454, 2010.
DOI : 10.1093/bioinformatics/btq454

S. Kurtz, Vmatch: large scale sequence analysis software, 2011.

. Mgescan-non-ltr, computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes, Nucl. Acids Res, vol.21, issue.37, p.143, 2009.

J. F. Lucier, RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures, Nucleic Acids Research, vol.35, issue.Web Server, pp.269-274, 2007.
DOI : 10.1093/nar/gkm313

N. Santiago, Genome-wide Analysis of the Emigrant Family of MITEs of Arabidopsis thaliana, Molecular Biology and Evolution, vol.19, issue.12, pp.2285-93, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004052

G. Myers, A fast bit-vector algorithm for approximate string matching based on dynamic programming, Ninth Combinatorial Pattern Matching Conference, vol.1448, pp.1-13, 1998.
DOI : 10.1007/BFb0030777

P. E. Warburton, Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes, Genome Research, vol.14, issue.10a, pp.1861-1870, 2004.
DOI : 10.1101/gr.2542904

Y. Chen, F. Zhou, G. Li, and . Xu, MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi, Gene, vol.436, issue.1-2, pp.1-7, 2009.
DOI : 10.1016/j.gene.2009.01.019

M. Han, Y. Et-wessler, and S. R. , MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences, Nucleic Acids Research, vol.38, issue.22, p.199, 2010.
DOI : 10.1093/nar/gkq862

S. V. Dongen, Graph Clustering Via a Discrete Uncoupling Process, SIAM Journal on Matrix Analysis and Applications, vol.30, issue.1, pp.121-141, 2008.
DOI : 10.1137/040608635

L. Yang and J. L. Et-bennetzen, Structure-based discovery and description of plant and animal Helitrons, Proceedings of the National Academy of Sciences, vol.106, issue.31, pp.12832-12839, 2009.
DOI : 10.1073/pnas.0905563106

N. Markham and M. Et-zuker, DINAMelt web server for nucleic acid melting prediction, Nucleic Acids Research, vol.33, issue.Web Server, pp.577-581, 2005.
DOI : 10.1093/nar/gki591

C. Charras and T. Et-lecroq, Handbook of exact string matching algorithms. s.l. : King's College publications, 2004.

S. Aluru and P. Et-ko, Handbook of Computational Molecular Biology. [éd.] S. Aluru. s.l. : Chapman & Hall/CRC Computer and Information Science Series, 2006.

N. Välimäki, Compressed suffix tree a basis for genome-scale sequence analysis, Bioinformatics, vol.23, issue.5, pp.629-659, 2007.
DOI : 10.1093/bioinformatics/btl681

V. Mäkinen, Compressed Suffix Tree. [En ligne] 2013

U. I. Manber and G. Et-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

A. M. Shrestha, M. C. Frith, and . Horton, A bioinformatician's guide to the forefront of suffix array construction algorithms, Briefings in Bioinformatics, vol.15, issue.2
DOI : 10.1093/bib/bbt081

P. Barenbaum, Efficient repeat finding in sets of strings via suffix arrays, Discrete Mathematics & Theoretical Computer Science, vol.2, issue.15, pp.59-70, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00980753

M. Burrows and D. J. Et-wheeler, A block sorting lossless data compression algorithm. Digital Equipment Corporation. Palo Alto : s.n, 1994.

P. Ferragina and G. Et-navarro, Compressed Indexes and their Testbeds. [En ligne] sept, 2005.

Y. Zhao, H. Tang, and . Et-ye, RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data, Bioinformatics, vol.28, issue.1, pp.125-126, 2012.
DOI : 10.1093/bioinformatics/btr595

. Fast, . Short, ?. Burrows, . Wheeler, H. Li et al., 14, s.l. : Oxford Pub, Bioinformatics, vol.25, pp.1754-1760, 2009.

L. Noe and . Kucherov, YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, pp.540-543, 2005.
DOI : 10.1093/nar/gki478
URL : https://hal.archives-ouvertes.fr/inria-00100004

J. R. Mora, Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo), BMC Plant Biol, vol.35, issue.10, 2010.

F. J. Sedlazeck, P. Rescheneder, and A. Et-von-haeseler, NextGenMap: fast and accurate read mapping in highly polymorphic genomes, Bioinformatics, vol.29, issue.21, pp.2790-2791, 2013.
DOI : 10.1093/bioinformatics/btt468

Z. Iqbal, De novo assembly and genotyping of variants using colored de Bruijn graphs, Nature Genetics, vol.44, issue.2, pp.226-232, 2012.
DOI : 10.1016/0198-8859(91)90078-N

P. Koch, M. Platzer, and B. Et-downie, RepARK--de novo creation of repeat libraries from whole-genome NGS reads, Nucleic Acids Research, vol.42, issue.9, 2014.
DOI : 10.1093/nar/gku210

G. S. Slater and . Birney, Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, vol.6, issue.1, pp.10-1186, 2005.

J. P. Ioannidis, Repeatability of published microarray gene expression analyses, Nature Genetics, vol.4, issue.2, pp.149-155, 2009.
DOI : 10.1097/EDE.0b013e31818131e7

K. Wolstencroft, The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud, Nucleic Acids Research, vol.41, issue.W1, pp.557-561
DOI : 10.1093/nar/gkt328

E. De-castro, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Research, vol.34, issue.Web Server, pp.362-365, 2006.
DOI : 10.1093/nar/gkl124

S. Datta and S. Et-mukhopadhyay, A Composite Method Based on Formal Grammar and DNA Structural Features in Detecting Human Polymerase II Promoter Region, PLoS ONE, vol.24, issue.6, 2013.
DOI : 10.1371/journal.pone.0054843.t006

T. Macke, RNAMotif: A new RNA secondary structure definition and discovery algorithm, Nucl Acids Res, vol.22, issue.29, pp.4724-4735, 2001.

J. Reeder, J. Reeder, and R. Et-giegerich, Locomotif: from graphical motif description to RNA motif search, Bioinformatics, vol.23, issue.13, pp.392-400, 2007.
DOI : 10.1093/bioinformatics/btm179

F. Meyer, Structator: fast index-based search for RNA sequence-structure patterns, BMC Bioinformatics, vol.12, issue.1, pp.10-1186, 2011.
DOI : 10.1093/bioinformatics/btp250

M. I. Abouelhoda, S. Kurtz, and . Ohlebusch, Replacing suffix trees with enhanced suffix arrays, Journal of Discrete Algorithms, vol.2, issue.1, pp.53-86, 2004.
DOI : 10.1016/S1570-8667(03)00065-0

T. Nussbaumer, MIPS PlantsDB: a database framework for comparative plant genome research, Database issue), pp.1144-51, 2013.
DOI : 10.1093/nar/gks1153

V. Brendel, Pattern Search. [En ligne, 2007.

K. Jensen, G. Stephanopoulos, and I. Et-rigoutsos, Biogrep: a multi?threaded pattern matcher for large pattern sets. kljensen/biogrep · GitHub. [En ligne, 2002.

R. Overbeek and . Scanformatches, En ligne] jul, 2010.

C. Belleannée, O. Sallou, and J. Et-nicolas, Application to the Modelling of -1 Ribosomal Frameshift events, Expressive Pattern Matching with Logol

A. Bousios, MASiVEdb: the Sirevirus Plant Retrotransposon Database, BMC Genomics, vol.13, issue.1, 2012.
DOI : 10.1093/molbev/msh057

P. Chen and J. , P-MITE: a database for plant miniature inverted-repeat transposable elements, Database issue), pp.1176-81, 2013.
DOI : 10.1093/nar/gkt1000

R. Li and R. , Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun, et al. PLoS Comput Biol, vol.4, issue.1, p.43, 2005.

C. R. Ouyang and S. Et-buell, The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants, Nucleic Acids Research, vol.32, issue.90001, pp.360-363, 2004.
DOI : 10.1093/nar/gkh099

F. M. You, RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development, Nucleic Acids Research, vol.38, issue.Web Server, pp.313-333, 2010.
DOI : 10.1093/nar/gkq425

E. De-castro, C. Sigrist, and A. Gattiker, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Research, vol.34, issue.Web Server, pp.362-365, 2006.
DOI : 10.1093/nar/gkl124

M. Nakagome, TIF): a novel program for detection of de novo transpositions of transposable elements, BMC Bioinformatics, vol.15, pp.10-1186