Yes, with a nested loop the problem is that you have to complete the inner loop before iterating the outer loop. So the inner loop is the problem. I've had time to look more closely at the data and have discovered some cases where there's a directed acyclic graph ( no multiedges ) with one source vertex, 21 vertices, 206 edges, and 165888 different paths!! The outer loop will traverse all those different arrays once whereas the inner loop will traverse them repeatedly doing list comparisons each time. Some of the suggestions here involve traversing the arrays just once and converting the data into a matrix that can be easily used to do list comparisons. Each of those 21 vertices will have a coordinate xy or list of coordinates giving its location in the matrix and so we can skip all the travsering. Makes sense to me so I'll try that one first. Thanks everyone for your help some good ideas.