The primary structure of a deoxyribonucleic acid (DNA) molecule is a sequence consisting of four types of letters, A, C., G, and T, each stands for a nucleotide. The length of such a DNA sequence ranges from several thousand letters for a simple virus to three billion letters for a human. We all know that these long and mysterious sequences encode Life as well as genetic diseases, but decoding the sequences is perhaps one of the most challenging tasks in the world. The ultimate goal of molecular biology is to understand what segments of a DNA are responsible for a biological function such as the color of eyes or a genetic disease such as cancer, and how these segments are formed and work. These functionally meaningful segments of a DNA are usually called genes. To find the genes which are responsible for some biological function, a biologist often compares a set of DNA sequences that share the same function and tries to identify regions which are “conserved” in all of these sequences. On the other hand, a biologist may also infer the “closeness” of two organisms by comparing their DNA sequences and computing the degree of similarity of the sequences. Such “closeness” information is useful in the reconstruction of evolutionary histories.