On the Expressivity of Alignment-Based Distance and Similarity Measures on Sequences and Trees in Inducing Orderings

Distance, Similarity and Sequence Comparison

“…However, distances and similarities are just vehicles that are used to create partitions of big sets of sequences and it is not at all clear that partitioning on the basis of distance will lead to the same partitioning as partitioning on the basis of similarities. Interestingly, Emms and Franco-Penya (2013) investigated precisely this problem, confined to edit-based distances and similarities. Remarkably, one of their conclusions is that partitions based on hierarchical clustering of distances can always be replicated by similarity-based hierarchical clustering but not vice versa: some similarity-based clusterings will not be replicable through distance-based hierarchical clustering.…”

Advances in Sequence Analysis: Theory, Method, Applications

“…However, distances and similarities are just vehicles that are used to create partitions of big sets of sequences and it is not at all clear that partitioning on the basis of distance will lead to the same partitioning as partitioning on the basis of similarities. Interestingly, Emms and Franco-Penya (2013) investigated precisely this problem, confined to edit-based distances and similarities. Remarkably, one of their conclusions is that partitions based on hierarchical clustering of distances can always…”