Which indices is the best for clustering analysis of DGGE band patterns?

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Fang Liu

Euclidean with permutation should work

Mohamed S. Sarhan

Euclidean distance and Bary-Curtis dissimilarity are suitable for your case, and both are widely used in DGGE gel analysis.

I do prefer Bary-Curtis dissimilarity because it is more usable in biological and ecological studies than Euclidean.