One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information.
Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon
Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files
Compute summary statistics for each TE family (number of TE copies, genome coverage...)
Ambiguous cases such as nested TE can be assembled into copies automatically or manually
Allow for working with a TE user-defined library
Allow for working with only a user-chosen set of TE families
