As the amount of computational time and memory space required increases exponentially with the number of sequences, it makes the multidimensional search matrix method computationally prohibitive to use for a large data set.

Multiple sequence alignment (MSA) is a tool used to identify the evolutionary relationships and common patterns between genes.

Topics include: Exhaustive Algorithms, Heuristic Algorithms, Needleman – Wunsch Algorithm, Progressive Methods of Multiple Sequence Alignment, Iterative Methods of Multiple Sequence Alignment, Localized Alignments in Sequences, Statistical Methods for Aiding Alignment, & Position – Specific Scoring Matrices.