E. Lander, L. Linton, B. Birren, C. Nusbaum, M. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.6, issue.6822, pp.860-921, 2001.
DOI : 10.1038/35057062

A. De-koning, W. Gu, T. Castoe, M. Batzer, and D. Pollock, Repetitive Elements May Comprise Over Two-Thirds of the Human Genome, PLoS Genetics, vol.25, issue.12, p.1002384, 2011.
DOI : 10.1371/journal.pgen.1002384.s013

P. Schnable, D. Ware, R. Fulton, J. Stein, F. Wei et al., The B73 Maize Genome: Complexity, Diversity, and Dynamics, Science, vol.326, issue.5956, pp.1112-1115, 2009.
DOI : 10.1126/science.1178534

URL : https://hal.archives-ouvertes.fr/hal-00751527

C. Sun, D. Shepard, R. Chong, J. Arriaza, K. Hall et al., LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders, Genome Biology and Evolution, vol.4, issue.2, pp.168-183, 2012.
DOI : 10.1093/gbe/evr139

C. Biémont and C. Vieira, Genetics: Junk DNA as an evolutionary force, Nature, vol.2, issue.7111, pp.521-524, 2006.
DOI : 10.1159/000084978

T. Wicker, F. Sabot, A. Hua-van, J. Bennetzen, P. Capy et al., A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, issue.12, pp.973-982, 2007.
DOI : 10.1038/nrg2165

URL : https://hal.archives-ouvertes.fr/hal-00169819

V. Kapitonov and J. Jurka, A universal classification of eukaryotic transposable elements implemented in Repbase, Nature Reviews Genetics, vol.8, issue.5, pp.411-412, 2008.
DOI : 10.1038/nrg2165-c1

C. Bergman and H. 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. Saha, S. Bridges, Z. Magbanua, and D. Peterson, Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences, Tropical Plant Biology, vol.104, issue.Suppl 1, pp.85-96, 2008.
DOI : 10.1007/s12042-007-9007-5

E. Lerat, Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs, Heredity, vol.38, issue.6, pp.520-533, 2010.
DOI : 10.1126/SCIENCE.1068037

URL : https://hal.archives-ouvertes.fr/hal-00539329

C. Chaparro and F. Sabot, Methods and Software in NGS for TE Analysis, Methods Mol Biol, vol.859, pp.105-114, 2012.
DOI : 10.1007/978-1-61779-603-6_6

L. Modolo and E. Lerat, Identification and analysis of transposable elements in genomic sequences In Genome analysis: Current Procedures and Applications, pp.165-181

A. Smit, R. Hubley, and P. Green, RepeatMasker Open-3.0. (http://www. repeatmasker.org), 1996.

S. Aparicio, J. Chapman, E. Stupka, N. Putnam, J. Chia et al., Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes, Science, vol.297, issue.5585, pp.1301-1310, 2002.
DOI : 10.1126/science.1072104

N. Juretic, T. Bureau, and R. Bruskiewich, Transposable element annotation of the rice genome, Bioinformatics, vol.20, issue.2, pp.155-160, 2004.
DOI : 10.1093/bioinformatics/bth019

T. Wheeler, J. Clements, S. Eddy, R. Hubley, T. Jones et al., Dfam: a database of repetitive DNA based on profile hidden Markov models, Nucleic Acids Research, vol.41, issue.D1, pp.70-82, 2013.
DOI : 10.1093/nar/gks1265

J. Jurka, Repbase Update: a database and an electronic journal of repetitive elements, Trends in Genetics, vol.16, issue.9, pp.418-420, 2000.
DOI : 10.1016/S0168-9525(00)02093-X

S. Tempel, . Using, and . Understanding-repeatmasker, Using and Understanding RepeatMasker, Methods Mol Biol, vol.859, pp.29-51, 2012.
DOI : 10.1007/978-1-61779-603-6_2

J. Ma, K. Devos, and J. Bennetzen, Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice, Genome Research, vol.14, issue.5, pp.860-869, 2004.
DOI : 10.1101/gr.1466204

S. Szak, O. Pickeral, W. Makalowski, M. Boguski, D. Landsman et al., Molecular archeology of L1 insertions in the human genome, Genome Biol, vol.3, pp.52-53, 2002.

V. Pereira, Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome, Genome Biology, vol.5, issue.10, p.79, 2004.
DOI : 10.1186/gb-2004-5-10-r79

V. Pereira, Automated paleontology of repetitive DNA with REANNOTATE, BMC Genomics, vol.9, issue.1, p.614, 2008.
DOI : 10.1186/1471-2164-9-614

V. Kapitonov and J. Jurka, Molecular paleontology of transposable elements in the Drosophila melanogaster genome, Proceedings of the National Academy of Sciences, vol.100, issue.11, pp.6569-6574, 2003.
DOI : 10.1073/pnas.0732024100

H. Yang, T. Hung, T. You, and T. Yang, Genomewide Comparative Analysis of the Highly Abundant Transposable Element DINE-1 Suggests a Recent Transpositional Burst in Drosophila yakuba, Genetics, vol.173, issue.1, pp.189-196, 2006.
DOI : 10.1534/genetics.105.051714

H. Quesneville, C. Bergman, O. Andrieu, D. Autard, D. Nouaud et al., Combined Evidence Annotation of Transposable Elements in Genome Sequences, PLoS Computational Biology, vol.16, issue.2, pp.166-175, 2005.
DOI : 1367-4803(2000)016[1040:MAPETR]2.0.CO;2

URL : https://hal.archives-ouvertes.fr/hal-00009013

C. Smith, S. Shu, C. Mungall, and G. Karpen, The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin, Science, vol.316, issue.5831, pp.1586-1591, 2007.
DOI : 10.1126/science.1139815

J. Kaminker, C. Bergman, B. Kronmiller, J. Carlson, R. Svirskas et al., The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective, Genome Biol, vol.320, pp.84-0084, 2002.

E. Kvikstad and K. Makova, The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important, Genome Research, vol.20, issue.5, pp.600-613, 2010.
DOI : 10.1101/gr.099044.109

R. Mills, E. Bennett, R. Iskow, and S. Devine, Which transposable elements are active in the human genome?, Trends in Genetics, vol.23, issue.4, pp.183-191, 2007.
DOI : 10.1016/j.tig.2007.02.006

. Bechet, ???One code to find them all???: a perl tool to conveniently parse RepeatMasker output files, Mobile DNA, vol.5, issue.1, p.13, 2014.
DOI : 10.1016/j.tig.2007.02.006