J. D. Thompson, J. E. Thierry, O. Poch, and O. , Rapid Scanning and Correction of Multiple Sequence Alignments, Bioinformatics, vol.19, 2003.

T. Jiang and L. Wang, On the Complexity of Multiple Sequence Alignment, J. Comput. BioI, vol.1, pp.337-378, 1994.

L. P. Bonizzoni and P. Gianluca, The Complexity of Multiple Sequence Alignment with SPscore that is a Metric, Theoretical Computer Science, vol.259, pp.63-79, 2001.

C. H. Papadimitriou and K. Steiglitz, Combinatorial Optimization: Algorithms and Complexity, 1998.

J. T. Horng, L. C. Wu, C. M. Lin, and B. H. Yang, A Genetic Algorithm for Multiple Sequence Alignment, Proc. LNCS, pp.407-420, 2005.

M. Hernández-guía, R. Mulet, and S. Rodríguez-pérez, A new Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem. The approach of polymers in a random media, Physical Review E, vol.72, pp.1-7, 2005.

C. W. Lei and J. H. Ruan, A Particle Swarm Optimization Algorithm for Finding DNA Sequence Motifs, Proc. IEEE, pp.166-173, 2008.

Z. J. Lee, S. F. Su, C. C. Chuang, and K. H. Liu, Genetic Algorithm with Ant Colony Optimization (GA-ACO) for Multiple Sequence Alignment, Applied Soft Computing, vol.8, pp.55-78, 2008.

L. Chen, L. Zou, and . Chen, An Efficient ant Colony Algorithm for Multiple Sequences Alignment, Proceedings of the 3rd International Conference on Natural Computation (ICNC '07), pp.208-212, 2007.

T. Riaz, Y. Wang, and K. B. Li, Multiple Sequence Alignment Using Tabu Search, Proceedings of 2nd Asia-Pacific Bioinformatics Conference (APBC), pp.223-232, 2004.

F. Xu1 and Y. Chen, A Method for Multiple Sequence Alignment Based on Particle Swarm Optimization, ICIC 2009, vol.5755, pp.965-973, 2009.

Y. Chen, J. Hu, K. Hirasawa, and S. Yu, Multiple Sequence Alignment Based on Genetic Algorithm with Reserve Selection, Proc. of Int. conf. on Networking, Sensing and Control (ICNSC), pp.1511-1516, 2008.

H. X. Long, W. B. Xu, J. Sun, and W. J. Ji, Multiple Sequence Alignment Based on a Binary Particle Swarm Optimization Algorithm, Proceedings of Fifth International Conference on Natural Computation, pp.265-269, 2009.

X. Lei, J. Sun, X. Xu, and L. Guo, Artificial Bee Colony Algorithm for Solving Multiple Sequence Alignment, Proc. of 2010 IEEE Fifth International Conference on BIC-TA, pp.337-342, 2010.

V. Cutello, G. Nicosia, M. Pavone, and I. Prizzi, Protein Multiple Sequence Alignment by Hybrid Bio-inspired Algorithms, Nucleic Acids Research, vol.39, issue.6, pp.1980-1992, 2011.
DOI : 10.1093/nar/gkq1052

URL : https://academic.oup.com/nar/article-pdf/39/6/1980/7186250/gkq1052.pdf

L. G. Ernesto and M. G. Lorena, Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment, ISRN Artificial intelligence, vol.2012, pp.1-6, 2012.

A. Abu-srhan, A. Daoud, and E. , A Hybrid Algorithm Using a Genetic Algorithm and Cuckoo Search Algorithm to Solve the Traveling Salesman Problem and its Application to Multiple Sequence Alignment, International Journal of Advanced Science and Technology, vol.61, pp.29-38, 2013.
DOI : 10.14257/ijast.2013.61.04

URL : https://doi.org/10.14257/ijast.2013.61.04

M. Kayaa, A. Sarhanb, and R. Alhajjb, Multiple Sequence Alignment with Affine Gap by using Multi-objective Genetic Algorithm, Computer Methods and Programs in Biomedicine, vol.114, pp.38-49, 2014.

J. Kennedy and R. Eberhart, Particle Swarm Optimization, Proceedings of IEEE International Conference on Neural Networks. 4, pp.1942-1948, 1995.

W. Ben-ameur, Computing the Initial Temperature of Simulated Annealing, Computational Optimization and Applications, vol.29, pp.369-385, 2004.
DOI : 10.1023/b:coap.0000044187.23143.bd

P. F. Rodriguez, L. F. Nino, and O. M. Alonso, Multiple Sequence Alignment Using Swarm Intelligence, International Journal of Computational Intelligence Research, vol.3, issue.2, pp.123-130, 2007.
DOI : 10.5019/j.ijcir.2007.96

URL : http://www.ripublication.com/ijcirv3/ijcirv3n2_2.pdf

C. Lamiche, An Effective Alignment Technique to Solve MSA Problem, Asian Journal of Mathematics and Computer, vol.17, issue.2, pp.2395-4213, 2017.

J. D. Thompson, F. Plewniak, and O. Poch, BAliBASE: A Benchmark Alignment Database for the Evaluation of Multiple Alignment Programs, Bioinformatics, vol.15, pp.87-88, 1999.

S. Lalwani, R. Kumar, and N. Gupta, A Novel Two-level Particle Swarm Optimization Approach for Efficient Multiple Sequence Alignment, Memetic Computing, vol.7, issue.2, pp.119-133, 2015.
DOI : 10.1007/s12293-015-0157-y

J. D. Thompson, P. Koehl, R. Ripp, and O. Poch, BAliBASE 3.0: Latest Developments of the Multiple Sequence Alignment Benchmark, Proteins, vol.61, issue.1, pp.127-136, 2005.
DOI : 10.1002/prot.20527

URL : https://hal.archives-ouvertes.fr/hal-00187785

J. D. Thompson, F. Plewniak, and O. Poch, A Comprehensive Comparison of Multiple Sequence Alignment Programs, Nucleic Acids Research, vol.27, issue.13, pp.2682-2690, 1999.
DOI : 10.1093/nar/27.13.2682

URL : https://academic.oup.com/nar/article-pdf/27/13/2682/7043210/27-13-2682.pdf