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This paper presents the combination of genetic algorithm and simulated annealing to solve multiple sequence alignment (MSA) assignment. Genetic algorithm will try to find a new region of feasible solution while simulated annealing will act as an aligning improver. There are several aspects that must be taken into consideration such as the representation, evaluation function and operator. Simulated annealing also helps to prevent local minima problem. Sequence similarity plays a major role in Bioinformatics and molecular biology. Significant results were produced from the prealignment and genetic algorithm phase.