ABSTRACT
An alignment (see Section 1.2.3) is a compact notation for the similarities and the differences between two or more sequences. To get the similar regions together, the alignment process allows the insertion of gaps into the sequences, so we will first discuss in Section 8.1 which data structures for storing gapped sequences are provided in SeqAn, before we propose the alignment data structures in Section 8.2. Algorithms for computing (global) alignments are explained in Sections 8.4 to 8.6.
