The number of Tranposable Elements included in the analysis is only a fraction of all the TEs present in the genomes or the copies have been all rearranged in the considered categories? It would be possible to include an higher number of Elements in such an analysis or there are particularly reasons to restrict it to this portion of TEs?
Article Evolutionary History of Mammalian Transposons Determined by ...
Their approach only works when a TE inserts into another TE. Thus, the vast majority of Alu elements do not have insertions in them and would not work. Basically, it will work best when the original element is either fairly long (not SINEs) and also fairly old, providing lots of opportunities for other elements to insert and disrupt them.
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