| allpairs_global | All-vs-all global alignment | |
| allpairs_local | All-vs-all local alignment | |
| pairs_global | Make pair-wise global alignments | |
| pairs_local | Make pair-wise local alignments | |
| sam_filter | Convert SAM alignments to BLAST6 or human-readable format | |
| search_pcr | Search for amplicons (matches to primer pairs) | |
| sortbylength | Sort by decresing sequence length | |
| sortbysize | Sort by decresing abundance (size= annotations) |