Repeats, and more particularly Transposable Elements (TEs) are major components of eukaryotes due to their effect at short and long terms on the genome evolution and species adaptation. It is thus important to be able to identify them in genome sequences to allow further analyses that can decipher their action. To perform these tasks, numerous tools have been developed to answer specific biological questions going from their annotation in assembled and non-assembled genome to polymorphic sequence variation among natural populations.