Multiple sequence alignment (MSA) is one of the topics of bio informatics that has seriously been researched. It is known as NP-complete problem. It is also considered as one of the most important and daunting tasks in computational biology. Concerning this a wide number of heuristic algorithms have been proposed to find optimal alignment. Among these heuristic algorithms are genetic algorithms (GA). The GA has mainly two major weaknesses: it is time consuming and can cause local minima. One of the significant aspects in the GA process in MSA is to maximize the similarities between sequences by adding and shuffling the gaps of Solution Coding (SC). Several ways for SC have been introduced. One of them is the Permutation Coding (PC). We propose a hybrid algorithm based on genetic algorithms (GAs) with a PC and 2-opt algorithm. The PC helps to code the MSA solution which maximizes the gain of resources, reliability and diversity of GA. The use of the PC opens the area by applying all functions over permutations for MSA. Thus, we suggest an algorithm to calculate the scoring function for multiple alignments based on PC, which is used as fitness function. The time complexity of the GA is reduced by using this algorithm. Our GA is implemented with different selections strategies and different crossovers. The probability of crossover and mutation is set as one strategy. Relevant patents have been probed in the topic.