Table 3. Comparison of the performances of PASTEC, REPCLASS, and TECLASS for classification to TE order level.

Dataset (sequence #)	Performance	PASTEC	PASTEC mapped to REPCLASS order (1)	PASTEC mapped to TECLASS order (2)	REPCLASS (3)	TECLASS (4)
Repbase-atha (318)
	Well classified	71.4	79.7	93.7	85.5	97.5
	Misclassified	10.2	1.9	2.5	2.8	1.9
	Not classified	18.4	18.4	3.8	11.6	0.6
Repbase-diff (5546)
	Well classified	51.3	59.1	49.7	66.9	47.7
	Misclassified	10.9	3.1	3.5	11.1	50.3
	Not classified	33.4	33.4	46.8	17.6	1.9
Repbase-all (9665)
	Well classified	22.4	31.9	8.6	12.4	40
	Misclassified	15.8	6.2	6.7	33.3	59.7
	Not classified	61.8	61.8	84.7	50.84	0.25

Note that the classification differs between the three tools. We therefore mapped the PASTEC classification results onto those for REPCLASS (1) and TECLASS (2). (2) Mapped onto TECLASS class I orders only. (3) order considered are: DNA transposon, LTR retrotransposon, helitron, non LTR retrotransposon. (4) order considered are only LTR, LINE/SINE.