The input control file contains the following 13 lines of data. 1. The first line contains input sequence file name. 2. The second line contains 1 integer parameter, start position for the folding segment. Default value is 1. 3. The third line contains 1 integer parameter, end position for the folding segment. Default value is the sequence length. 4 An interger parameter, the total number of SER used in the calculation. Default value is 50. 5. Ratio of the structure similarity, Default value is 0.9. If the structure similarity between two structures is greater than the value, they are classified in the same group. 6. An interger parameter, Default value is 1. It means that those predictions will be ranked within 1.96 std leavel. 7. A chracter "N", a fixed chracter. 8. "Y" is a default character. It means you want to output all predictions in the fole of effold.reg by region table, then you have to input the file name in the next line. If the character is "Y" you don't need to input the file name in the next line. 9. File name of the region table for all predictions computed by SERs. 10. File name of a list that contains all possible occurring stems with the occurring frequency found in the simulation. 11. A text file for the structure classification. 12. A region table file with annotation for all classified group structure computed in the simulation. 13. A chracter "N", a fixed chracter.