Table 2.

Comparison of existing classification tools.

Software	URL	TE type	Interface	Remark
TEclass	http://www.compgen.uni-muenster.de/teclass	DNA transposons, LTRs, LINEs, SINEs	Command line	The input should not contain more than a few thousand sequences. The entered data must not exceed 1MB in size.
LTRSift	http://www.zbh.uni-hamburg.de/?id=378	LTRs	Graphical/Desktop	gff3 file (annotation data) is required, it could be generated by LTRHarvest and LTRdigest.
RepClass	https://sourceforge.net/projects/repclass	DNA transposons, LTRs, non-LTRs, Hélitrons	Command line	Dependencies: wu-blast. No documentation available about installation or usage.
PASTEC	https://urgi.versailles.inra.fr/Tools/PASTEClassifier	DNA transposons, LTRs, non-LTRs, Hélitrons	Command line	Pastec is the REPET package Transposable Elements classifier used in the TEdenovo pipeline, and the corresponding standalone tool is PASTEClassifier.py.