<p>I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them. I am currently trying to use RepeatMasker to identify them using a clade specific library from RepBase but I was thinking of trying to look for them de novo with REPET. Just looking for suggestions and ideas really. Thank you.</p>

Tandem Repeat Finder is also a good option for finding denovo repeats.

You can also try, Censor for finding different kinds of repeats from your sequences. Check <a href="http://www.ncbi.nlm.nih.gov/pubmed/19378152">this paper</a> analysing transposons using censor and repeatmasker.