Ok, your script is nearly there, but you need to be able to store many neighbors for each element, so instead of a hash you need a HashofHashes, see perllol. Just change lines like $h{$element}=$domains1[1]; and replace them with $h{$element}{$domains1[1]}++;

Why do I have the impression this is just homework? Maybe because a similar question, just with words instead of domains, was posted inside an hour of this one.