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Multiple sequence alignment (MSA) is an alignment of three or more sequences. Ordinarily, sequences one above the other can produce the final alignment. This paper focuses on solving the Multiple Sequence Alignment (MSA) problem by using a Flower Pollination Algorithm (FPA) that is hybridised with the profile technique. The FPA is considered a new meta-heuristic method based on a particular population. MSA is used in numerous applications, for example, an identification of conserved motifs, phylogenetic analysis, protein structure prediction and genome primer identification. In a study related to the MSA, a major challenge is attempting to propose a method for maximising the Sum-of-Pairs (SP) score and Column Score (CS) in order to obtain the most optimised MSA method. Accordingly, a profile technique is proposed to increase the quality of the MSA. The outcomes are compared against 7 other …