I applied number of methods of clustering, and I want to evaluate these different methods using Dunn index, in this method I have to calculate the distance among clusters and among points in clusters.
My question is: if my algorithm is clustering users depending on their sequences, i.e., each user has sequences, then the algorithm measures the similarity among sequences using seq. alignment technique, then cluster them. Sequence alignment tool considers two users most similar when they have max score. If my clusters are id's of users or sequences of users, how do I compute the distance among clusters and among sequences within a cluster?