It sounds like the master is a "template" though, and the files need to be in a similar format, but not exactly the same. In which case, tools like sum/cksum/gpg would not be useful because they would return a completely different result if one single byte differs between the compared files.
Perhaps you could set up the template file as a big regex basically, replacing the parts where varying data is expected with appropriate search strings. Some sample input files would help us advise you.
Annihilannic.