i gues you r talking about PHASE, a haplotype reconstructing software. I am not sure of all the details of this program. But some similar programs are 16 bit (MS-DOS) based, and the exe files run in XP. for vista 64 bit, there is almost no way to run that program (unless u use virtual PC) , in in 32 bit vista it might run. The best way to run these type of programs is of course in LINUX where they are built what about making a live CD of Ubuntu , or even u can emulate linux inside windows (http://lifehacker.com/5195999/portable-ubuntu-runs-ubuntu-inside-windows)

and if u r talking about PHASE here is manual which i think u have already downloaded. (http://stephenslab.uchicago.edu/instruct2.1.pdf)