, Bioinformatics and Management Science: Some Common Tools and Techniques, Operations Research, vol.52, issue.2, pp.165-190, 2004.
DOI : 10.1287/opre.1030.0095
, BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations, Nucleic Acids Research, vol.29, issue.1, pp.323-326, 2001.
DOI : 10.1093/nar/29.1.323
URL : https://academic.oup.com/nar/article-pdf/29/1/323/9905805/290323.pdf
, An ant colony optimization algorithm for DNA sequencing by hybridization, Computers & Operations Research, vol.35, issue.11, pp.3620-3635, 2008.
DOI : 10.1016/j.cor.2007.03.007
, Protein multiple sequence alignment by hybrid bio-inspired algorithms, Nucleic Acids Research, vol.13, issue.2, pp.1980-1990, 2010.
DOI : 10.1089/cmb.2006.13.309
URL : https://academic.oup.com/nar/article-pdf/39/6/1980/7186250/gkq1052.pdf
, ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Research, vol.15, issue.2, pp.330-340, 2005.
DOI : 10.1101/gr.2821705
URL : http://genome.cshlp.org/content/15/2/330.full.pdf
, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340
URL : https://academic.oup.com/nar/article-pdf/32/5/1792/7055030/gkh340.pdf
, Progressive sequence alignment as a prerequisite to correct phylogenetic trees, Journal of Molecular Evolution, vol.24, issue.4, pp.351-360, 1987.
DOI : 10.1007/bf02603120
, A user's guide to tabu search, Annals of Operations Research, vol.17, issue.1, pp.3-28, 1993.
DOI : 10.1007/BFb0121086
, Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments, Journal of Molecular Biology, vol.264, issue.4, pp.823-838, 1996.
DOI : 10.1006/jmbi.1996.0679
, Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment, Journal of Computational Biology, vol.2, issue.3, pp.459-472, 1995.
DOI : 10.1089/cmb.1995.2.459
, Multiple sequence alignment, Protein Structure Prediction -Methods and Protocols, 2000.
, Upcoming challenges for multiple sequence alignment methods in the high-throughput era, Bioinformatics, vol.21, issue.Suppl. 1, pp.2455-2465, 2009.
DOI : 10.1093/bioinformatics/bti582
, Multiple sequence alignment using simulated annealing, Bioinformatics, vol.10, issue.4, pp.419-472, 1994.
DOI : 10.1093/bioinformatics/10.4.419
, A review on particle swarm optimization variants and their applications to multiple sequence alignments, Journal of Applied Mathematics and Bioinformatics, vol.3, issue.2, pp.87-124, 2013.
, A new greedy randomized adaptive search procedure for multiple sequence alignment, International Journal of Bioinformatics Research and Applications, 2011.
DOI : 10.1504/ijbra.2013.054695
, A Tabu Search Approach to Multiple Sequence Alignment, 2008.
, A tool for multiple sequence alignment., Proc. Natl. Acad. Sci, pp.4412-4415, 1989.
DOI : 10.1073/pnas.86.12.4412
URL : http://www.pnas.org/content/86/12/4412.full.pdf
, SAGA: sequence alignment by genetic algorithm, Nucleic Acids Research, vol.24, issue.8, pp.1515-1524, 1996.
DOI : 10.1093/nar/24.8.1515
URL : https://academic.oup.com/nar/article-pdf/24/8/1515/6964040/24-8-1515.pdf
, T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000.
DOI : 10.1006/jmbi.2000.4042
, COFFEE: an objective function for multiple sequence alignments, Bioinformatics, vol.14, issue.5, pp.407-422, 1998.
DOI : 10.1093/bioinformatics/14.5.407
URL : https://academic.oup.com/bioinformatics/article-pdf/14/5/407/9731908/140407.pdf
, High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools, Parallel Computing, vol.42, p.10, 2014.
DOI : 10.1016/j.parco.2014.09.010
URL : https://repositori.udl.cat/bitstream/10459.1/48329/1/021620.pdf
, An iterative method for faster sum-of-pairs multiple sequence alignment, Bioinformatics, vol.16, issue.9, pp.808-814, 2000.
DOI : 10.1093/bioinformatics/16.9.808
, Multiple sequence alignment using tabu search, Proceeding of Asia-Pacific Bioinformatics Conference, pp.1-10, 2004.
, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, issue.4, pp.406-425, 1987.
, Multiple Sequence Alignment with Evolutionary Computation, Genetic Programming and Evolvable Machines, vol.5, issue.2, pp.121-144, 2004.
DOI : 10.1023/B:GENP.0000023684.05565.78
, PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information, Nucleic Acids Research, vol.33, issue.Web Server, pp.289-294, 2005.
DOI : 10.1093/nar/gki390
URL : https://academic.oup.com/nar/article-pdf/33/suppl_2/W289/7622741/gki390.pdf
, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673
, A web server for multiple sequence alignment using genetic algorithm, Genome Informatics, vol.12, pp.382-383, 2001.
, SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures, Bioinformatics, vol.58, issue.2, pp.3615-3621, 2005.
DOI : 10.1002/prot.20308
URL : https://academic.oup.com/bioinformatics/article-pdf/21/18/3615/520785/bti582.pdf