CPAN Algorithm::Diff method:

    time to compare same two files 1000 times:

    40.28 sec
    39.68 sec
    39.97 sec
    40.17 sec
    39.70 sec
    
    39.71 sec
    39.61 sec
    39.82 sec
    39.71 sec
    39.60 sec
    
    avg. = 39.83 sec

diffutils method:

    time to compare same two files 1000 times:
    
    11.68 sec
    11.72 sec
    11.63 sec
    11.69 sec
    11.78 sec
    
    11.62 sec
    11.62 sec
    11.78 sec
    11.66 sec
    11.62 sec
    
    avg. = 11.68 sec