Alignment Algorithms ( e.g. Pairwise and Multiple ) are one of the core algorithms in SeqAn. In this section you can learn how SeqAn represents alignments as C++ Objects and how you could use those data structures for your own alignment algorithm. Furthermore, you can learn which different kinds of Scoring Schemes exist, i.e. which combinations of Match/Mismatch Evaluation (e.g. Simple Score, Substitutional Matrices Score) and Insertion/Deletion Evaluation (e.g. Linear Gap Model, Affine Gap Model and Dynamic Gap Model) are possible and how you can define your own Scoring Matrices.