| Program name | Description |
| matcher |
Waterman-Eggert local alignment of two sequences
|
| seqmatchall |
All-against-all word comparison of a sequence set
|
| supermatcher |
Calculate approximate local pair-wise alignments of larger sequences
|
| water |
Smith-Waterman local alignment of sequences
|
| wordfinder |
Match large sequences against one or more other sequences
|
| wordmatch |
Find regions of identity (exact matches) of two sequences
|
| domainalign |
Generate alignments (DAF file) for nodes in a DCF file
|
| domainrep |
Reorder DCF file to identify representative structures
|
| seqalign |
Extend alignments (DAF file) with sequences (DHF file)
|
| oalistat |
Statistics for multiple alignment files
|