|   | ALIGNMENT LOCAL | 
Local sequence alignment
| 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 |