| Alignment Program |
| ALN | Overview | Online |
| Pairwase alignment of biological sequences supporting spliced alignment procedures |
| PRRN | Overview | Online |
| Multiple sequence alignment by doubly nested randomized iterative method |
| SPALN | Overview | Online |
| Mapping and Alignment of a set of cDNA sequences onto a genomic sequence |
| ALNGG | Overview | Online |
| Exon finding by genomic sequence comparison |