| Description | Matrix |
|---|---|
| Standard similarity matrix (20 amino acid types) | JO20.sim (text) |
| Reduced WW5 similarity matrix (5 amino acid types: Wang and Wang) | WW5.sim (text) |
| Reduced SR5 similarity matrix (5 amino acid types: Solis and Rackovsky) | SR5.sim (text) |
| Reduced MU4 similarity matrix (4 amino acid types: Murphy et al.) | MU4.sim (text) |
| Reduced MM5 similarity matrix (5 amino acid types: Melo and Marti-Renom) | MM5.sim (text) |
| Random similarity matrices(5 amino acid types: Random grouping) | FTP files (text) |