Thanks. I don't have bdiff, and comm didn't quite work... not sure why. I ran it (took awhile) and checked one of the first lines in the output... it was in both files. So that isn't what I wanted either. The ordering in the two files is close, but not perfect (that is, one could have abcd and the other adbc, but the distance should be limited to within a couple hundred lines). I suspect I'll have to write a custom script for this, but I could use some help.