There are many complete sequenced genomes, it needs a lot of efforts to discover the contents and the fine structures of those genomes. I am looking for an effective and easy method to mine the wealth of information in those genomes to discover retrotransposons.
The approach will likely depend strongly on the specifics of your search, as in what types of retrotransposons are you searching for?
As for a general source from which you can search for genome signatures of many/all known retroelements in many different genomes I know not; that you will likely have to write yourself, or at least create a pipeline that strings together other tools.
For LTR-Rts you may be interested in the attached link. I know there is also one written for find DIRS1-like retroelements that I used once.
Anyways my point is that you may not find a premade general-purpose tool, but if you can limit the scope of your search a bit you can find a lot of useful tools already written.
edit, added a few more links
http://tlife.fudan.edu.cn/ltr_finder/
http://www.drive5.com/piler/
http://www.girinst.org/downloads/software/censor/
http://www.repeatmasker.org/
Hi, you can take a look at the REPET package which is a pipeline that use the tools presented in the first answer. It is quite easy to install and it can run on a local machine.
Also, you could use RepeatScout or RepeatModeler.
But of course, as stated before you have to choose the right method in accordance with your data.
Hope it helps
https://urgi.versailles.inra.fr/Tools/REPET
http://bix.ucsd.edu/repeatscout/
http://www.repeatmasker.org/RepeatModeler.html
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