List of RNA structure prediction software Comparative methods Comparative methods

| Name_ | Number_of_sequences_Number_of_sequences_ | Alignment_Alignment_predicts_an_alignment_ | Structure_Structure_predicts_structure_ | Knots_Knots_Pseudoknot_prediction_ | Link |
|---|---|---|---|---|---|
| Carnac | any | no | yes | no | sourcecode, webserver |
| CentroidAlifold | any | no | yes | no | sourcecode webserver |
| CentroidAlign | any | yes | no | no | sourcecode |
| CMfinder | 3le seqs le60 | yes | yes | no | sourcecode, webserver, website |
| CONSAN | 2 | yes | yes | no | sourcecode |
| DAFS | any | yes | yes | yes | sourcecode |
| Dynalign | 2 | yes | yes | no | sourcecode |
| FoldalignM | any | yes | yes | no | sourcecode |
| FRUUT | any | yes | input | no | sourcecode, webserver |
| GraphClust | any | yes | yes | no | sourcecode |
| KNetFold | any | input | yes | yes | linuxbinary, webserver |
| LARA | any | yes | yes | no | sourcecode |
| LocaRNA | any | yes | yes | no | sourcecode, webserver |
| MASTR | any | yes | yes | no | sourcecode |
| Multilign | any | yes | yes | no | sourcecode |