| 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 |
| mse | Multiple Sequence Editor |