I already installed java ,j2sdk 1.4.1_01 on a windows XP platform, and downloaded the package, smithwaterman and unpacked into a directory c:\applications\java/. I just clicked 'c:\applications\java\smithwaterman\class\run.bat' but it did not work. Next time, I copied the run.bat to it's parent directory, and I clicked again 'c:\applicaations\java\smithwaterman\run.bat' then, it looked lake it worked. I could see a window and I selected and typed parameters required then finally clicked the start button, but it did vomit errror messages on the prompt window. I do not know what happened. This must be a stupid question, but I need some help. would you give me some comment?