Table 2.
Percentage of 454 Shotgun Data Classified Using Different Methods
| Species | RepeatMasker/RepBase (%) | RepeatModeler/REPCLASS (%) | Our TE-Mining Method (%) | Our TE-Mining Method (% unclassified repeats)a |
| Aneides flavipunctatus | 1.91 | 23.90 | 47.52 | 15.01 |
| Batrachoseps nigriventris | 1.29 | 16.92 | 39.39 | 7.57 |
| Eurycea tynerensis | 1.15 | 9.81 | 25.18 | 8.09 |
| Desmognathus ochrophaeus | 0.16 | 9.41 | 39.69 | 11.98 |
| Bolitoglossa rostrata | 1.15 | 3.50 | 30.18 | 17.79 |
| Bolitoglossa occidentalis | 1.64 | 4.35 | 33.19 | 8.38 |
a
For comparison, we also show the percentage of data identified by our method as nonsimple repeats, but not classified as known TE sequence.