There are many ballistics programs out there. I've even written a few, myself. Some are free and some cost a little money. Some cost more. Some allow you to specify the actual point height of your sight and others offer only a couple of standard heights.
I use the Speer Balistics Calculator (slide rule) these days, because I am so familar with my loads I don't need the fine detail, any more.
Drop over to Steves pages for a pretty good list of programs he has vetted.
Do a google on "ballistics programs download" for bunches of them.
Drop in on AmmoGuide for more information than you will ever need.
The only major difference you will see with changing the calculations to account for the height of the aiming spot on your sight is in the point at which the bullet crosses the line of sight. The curve the bullet takes from muzzel to ground will remain the same. Each rifle and bullet and load is enough different that you are going to calculate only an approximation, anyway. The ballistic program will get you close, but the actual calculations with YOUR rifle and YOUR load are taken from the holes in your paper.