| Program name | Description |
| edialign |
Local multiple alignment of sequences
|
| emma |
Multiple sequence alignment (ClustalW wrapper)
|
| infoalign |
Display basic information about a multiple sequence alignment
|
| plotcon |
Plot conservation of a sequence alignment
|
| prettyplot |
Draw a sequence alignment with pretty formatting
|
| showalign |
Display a multiple sequence alignment in pretty format
|
| tranalign |
Generate an alignment of nucleic coding regions from aligned proteins
|
| eomega |
Multiple sequence alignment (ClustalO wrapper)
|
| eomegapp |
Profile with profile (ClustalO wrapper)
|
| eomegaps |
Single sequence with profile (ClustalO wrapper)
|
| eomegash |
Sequence with HMM (ClustalO wrapper)
|
| eomegasp |
Sequence with profile (ClustalO wrapper)
|
| mse |
Multiple sequence editor
|