Distance, Similarity and Sequence Comparison

Abstract

In this chapter we focus on the axiomatic foundations of and the relations between two fundamental concepts of sequence analysis: distance and similarity. We discuss and interpret each of the individual axioms and point out their relevance in practical application. We will discuss units of distance, admissible transformations and normalization as a method that allows for interpreting the size of distances and similarities. We also discuss how similarity and distance can be derived from each other and, in passing, we deal with some quite common misunderstandings pertaining to these concepts.