Umm, Wuqiong, your question's actually answered in the instruction manual
Octal digits. In this order: UDFBLRESM. So, say you want an RU 2-gen algorithm, your binary code would be 100001000 (each digit stands for U, D, F, B, L, R, E, S, M respectively), convert that to a 3-digit octal code, which is 410 (you can do this easily with a pen and paper, or you could use a calculator if you're lazy), and place that digit before your cubie sequence.
Another example, say you're looking for an OH alg, and you want to restrict moves to RUL, your binary code is 100011000, converted to octal code that's 430.
Fanwuq:
I got it to run but now how do I make the cube configeration. like it say UF UR UB UL etc. but what do I type underneith them?
Sorry Wuqiong, I'm stealing your question

Easy! Just type whatever your cube looks like. Say you want an algorithm for a Y-perm, you would type this:
Code:
UF UR UB UL DF DR DB DL FR FL BR BL UFR URB UBL ULF DRF DFL DLB DBR
! ! UL UB !! UBL ! UFR !!
The first line is what is given in the program, don't type that, just type the second line.
Most important thing is you've gotta type the cubie that's in that position, not what position that cubie is in. That was confusing, I know. Example, you type in the order UF UR UB ... right? So you should type the sticker of the cubie that's in the UF position, then the sticker of the cubie that's in the UR position, then the sticker of the cubie that's in the UB position, etc. NOT the position of the UF sticker, then the position of the UR sticker, then the position of the UB sticker, get it? I'm telling you what it is and what it's not because I myself was confused in the beginning. Read the readme to find out what "!" "?" "@" etc. mean, there's a lotta weird syntax you have to get used to.