I applied number of methods of clustering  , and I want to evaluste these differnt methods using Dunn index  ,in this nethod I have to calculate the distance among clusters and among points in clusters.

my query is  : if my algorithm is clustering users deoending on their sequences, i.e each user has sequences  , then the algorithm measure the similarity among sequences using seq. alignment technique  , then cluster them. Sequence alignment tool consider most similar between two users when they have max score. if my clusters are id's of users or sequences of users  , how compute the distance among clusters and among sequuences within cluster?

thanks

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?