I would like to characterise retroelements (retrotransposons) across several plant genomes. I don't have any experience with identification and classification of repetitive elements. Can you recommend me some tools or some good reads focusing on the topic?
LTRharvest is a tool specifically designed to find LTR retrotransposons in large genomes.
Also RepeatMasker detect retrotransposons among many other repetitive sequences.