Insertions and deletions are observed within protein families, and it is normally necessary to introduce such indels when producing an alignment. The simplest scheme for gaps introduces a new character that scores u when aligned with any amino acid. Since gaps are comparatively rare, u is usually made negative. As a consequence, u is often referred to as the gap-penalty. In this simple scheme, a gap of 10 residues is penalised 10 times more highly than a gap of 1 residue. Within protein families, this makes little sense, since gaps of more than one residue are needed to obtain structurally reasonable alignments. The most commonly used scoring scheme for gaps is a function of the form: ul + v, where l is the length of the gap in residues. This form of penalty function is referred to as affine and has efficiency advantages over more elaborate penalty functions [Gotoh, 1982]. The constants v and u are often referred to as the penalties for creation and extension of the gap, or length-independent and length-dependent penalties, respectively. Gap penalties need not be uniform across the sequence and such position specific gap penalties are discussed in Section 4.4.