T-lex

Transposable Element annotation using Next-Generation Sequencing data

The T-lex package contains two pipelines. The T-lex pipeline calls presence/absence of known TE insertions using re-sequencing data. On top of the genotyping, this pipeline also allows to re-annotate TEs and discover traces of transposition events called Target Site Duplication (TSD).
The other T-lex pipeline discovers and annotates de novo TE insertions.

http://petrov.stanford.edu/cgi-bin/Tlex.html

T-lex Web Site