Zaxo is correct. I also use Algorithm::Diff to great extend. It is simple to use (once you understand the nested Array structure) and acts like Unix Diff.
To increase the speed, I suggest following method.
1) First compare lines exactly as string compare, if they are same then just move ahead to next sets of lines.
2) If the lines are NOT same then use Algorithm::Diff to understand difference.
Regards,
SanPerl