The major drawback of the progressive and iterative alignment strategies is that they are largely global alignment based and may therefore fail to recognize conserved domains and motifs among highly divergent sequences of varying lengths.

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.