How can I evaluate the clusters that result from sequence alignment?

I used sequence alignment to find the similarities among a set of objects, then used agglomerative clustering to cluster the sequences. At the same time I used another way for clustering the sequences.

• Are there ways to evaluate the resultant clusters that result from sequence alignment?
• And if I used Dunn index measure for evaluation, how I can compute the distance among clusters?
• And how do I compute the distance between the centroids?
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