| AnnSpec | a pattern factory that uses the AnnSpec program (version 2.1) |
| Elph | a pattern factory that uses the Elph program |
| Gibbs | a pattern factory that uses Chip Lawrences Gibbs program |
| MEME | a pattern factory that uses the MEME program |
| SimplePFM | a simple position frequency matrix factory |
| YMF | a pattern factory that uses the MEME program |