I have used R to calculate a similarity matrix for 11 proteins (histones) from a fasta file. Then I need to turn the similarity matrix into a distance matrix in order to use it in hclust. I have used sim2dist and also dist with all methods (euclidean, maximum, manhattan, canberra, binary, minkowski). I have excluded the binary method but I am not sure which is the best way to calculate the distance from the rest of my options. Any thoughts?