# Bioinspired Algorithms for Multiple Sequence Alignment:
## 7 Conclusions and Discussion  
In this study, we presented a systematic literature review on bioinspired-based methods for solving the MSA problem that can guide researchers and practitioners in understanding the challenges and new trends in the area. In particular, many bioinspired-based techniques were examined, emphasizing the MSA. The study used the SLR method, which thoroughly analyzes and synthesizes the published articles. We considered studies conducted from 2010 to 2024 to provide more recent and comprehensive developments. After collecting and examining several studies, 45 papers were found after eligibility screening and quality assessment. The results showed that the Genetic Algorithm and Memetic Optimization are the most used bioinspired-based algorithms applied for solving MSA problem with 49%, followed by the Memetic Algorithm representing 13% of the total papers identified for the MSA solutions. Next is the PSO, which accounts for 11% of the total articles identified in the review, followed by the BO and BFO, which represent 5% of each of the total number of bioinspired-based algorithms applied for solving the MSA problem. Finally, we can see that based on the reviewed literature, the Simulated Annealing algorithm is the least utilized algorithm with 2% of the total reviewed papers. Furthermore, the results of the performance evaluation measures used for the MSA problem were illustrated. Figure 8 shows that several benchmark datasets are used to validate the effectiveness of the Multiple Sequence Alignment solutions. Based on the articles from the literature selected for the proposed SLR study, the most popular benchmark techniques include BAliBASE, SABmark, HOMSTRAD, OXBench, and Prefab. The figure shows that the most commonly applied benchmark datasets are BAliBASE and SABmark, with 64% and 13%, respectively, followed by OXBench and Prefab with 10% each. Finally, HOMSTRAD has been identified as the least benchmark dataset for the MSA with a 3% use case. Moreover, the proposed review shows the performance evaluation measures used for the MSA problem among the reviewed papers. Figure 9 shows that several performance quality measures were used to validate the effectiveness of the Multiple Sequence Alignment solutions. Based on the published papers from the literature selected for the proposed SLR study, the most popularly used performance quality evaluation measures include structural-based techniques, simulated-based approaches, and consistency-based approaches. Figure 9 shows that structural techniques based on the idea that amino acid residues corresponding to the same position in the three-dimensional structure should be aligned are the most popular quality measures for MSA with 73%. Next is consistency, which is predicated on the notion that two residues are probably accurately aligned if many software programs reliably align them with 17%; finally, the simulation-based techniques, which use a probabilistic model to simulate sequence evolution and produce evolved sequences and reference alignments, come with 10%. Additionally, we examined the open issues of the study, which include the creation of more potent algorithms based on parallel and distributed paradigms, as well as the blending of various algorithms; the creation of more resilient algorithms that consider the uncertainty or stochasticity present in bioinformatics; the development of frameworks for parameter fine-tuning to take advantage of instance-specific aspects to improve results; and the application of multi-objective techniques to take into account the various objectives in the majority of issues. Finally, the last section of the proposed systematic literature review (SLR) outlines several study limitations. These limitations include the targeted sources, predominantly journals and conferences. Additionally, the review was limited to English-language publications, potentially excluding valuable contributions from non-English sources. Moreover, the primary databases used for the review may have influenced the scope of the findings.