| Software | Function | Pseudo-knot |
|---|---|---|
| SCARNA | Pairwise Structural Alignment | yes |
| Murlet | Multiple Structural Alignment | no |
| MXSCARNA | Multiple Structural Alignment | no |
| RNAmine | Structural Motif Extraction | no |
| PHMMTS | Sequence-structure alignment | no |
| PSTAG | Sequence-structure alignment | yes |