Article Outline
Abstract
Introduction
Phylogenetic Analysis
Methods Based on Pairwise Distance
Parsimony Methods
Maximum Likelihood Methods
Multiple Sequence Alignment
Scoring Alignment
Alignment Approaches
Progressive Algorithms
Graph-Based Algorithms
Iterative Algorithms
Novel Graph-Theoretical Genomic Models
Definitions
Construction of a Conflict Graph from Paths of Multiple Sequences
Complexity Theory
Special Cases of MWCMS
Computational Models: Integer Programming Formulation
Summary
Acknowledgement
References
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References
Abbas A, Holmes S (2004) Bioinformatics and management science: Some common tools and techniques. Oper Res 52(2):165–190
Althaus E, Caprara A, Lenhof H, Reinert K (2006) A branch-and-cut algorithm for multiple sequence alignment. Math Program 105(2-3):387–425
Altschul S (1991) Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 219(3):555–565
Altschul SF, Carroll RJ, Lipman DJ (1989) Weights for data related by a tree. J Mol Biol 207(4):647–653
Bains W, Smith G (1988) A novel nethod for DNA sequence determination. J Theor Biol 135:303–307
Barton GJ, Sternberg MJE (1987) A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons. J Mol Biol 198:327–337
Blazewicz J, Formanowicz P, Kasprzak M (2005) Selected combinatorial problems of computational biology. Eur J Oper Res 161:585–597
Bonizzoni P, Vedova G (2001) The complexity of multiple sequence alignment with SP-score that is a metric. Theor Comput Sci 259:63–79
Bos D, Posada D (2005) Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol 29(3):211–227
Bruno WJ, Socci ND, Halpern AL (2000) Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17:189–197
Carrillo H, Lipman D (1988) The multiple sequence alignment problem in biology. SIAM J Appl Math 48(5):1073–1082
Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH (2006) Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res 34(9):2598–2606
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 31(13):3497–3500
Chor B, Tuller T (2005) Maximum likelihood of evolutionary trees: hardness and approximation. Bioinf 21(Suppl. 1):I97–I106
Clote P, Backofen R (2000) Computational Molecular Biology: An Introduction. Wiley, NY, USA
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nature reviews. Genet 6(5):361–375
Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological Sequence Analysis. Cambridge University Press, UK
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376
Felsenstein J (1988) Phylogenies from molecular sequences: Inference and reliability. Annu Rev Genet 22:521–565
Felsenstein J (1989) PHYLIP – phylogeny inference package (version 3.2). Cladistics 5:164–166
Fitch WM (1971) Toward defining the course of evolution: Minimum change for a specific tree topology. Syst Zool 20(4):406–416
Gallant J, Maider D, Storer J (1980) On finding minimal length superstrings. J Comput Syst Sci 20:50–58
Garey M, Johnson D (1979) Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, San Francisco, USA
Gascuel O (1997) BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14(7):685–695
Goeffon A, Richer J, Hao J (2005) Local search for the maximum parsimony problem. Lect Notes Comput Sci 3612:678–683
Golumbic MC, Rotem D, Urrutia J (1983) Comparability graphs and intersection graphs. Discret Math 43:37–46
Gotoh O (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 264(4):823–838
Gotoh O (1999) Multiple sequence alignment: algorithms and applications. Adv Biophys 36:159–206
Grötschel M, Lovász L, Schrijver A (1984) Polynomial algorithms for perfect graphs. Annals Discret Math 21:325–356
Grötschel M, Lovász L, Schrijver A (1988) Geometric algorithms and combinatorial optimization. Springer, New York
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696–704
Gupta S, Kececioglu J, Schaeffer A (1995) Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J Comput Biol 2:459–472
Hein J (1989) A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol Biol Evol 6(6):649–668
Huelsenbeck J, Crandall K (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 28:437–66
Hughey R, Krogh A (1996) Hidden markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 12(2):95–107
Idury RM, Waterman MS (1995) A new algorithm for DNA sequence assembly. J Comput Biol 2(2):291–306
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian Protein Metabolism. Academic Press, New York, pp 21–123
Just W, Vedova G (2004) Multiple sequence alignment as a facility-location problem. INFORMS J Comput 16(4):430–440
Keane T, Naughton T, Travers S, McInerney J, McCormack G (2005) DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinf 21(7):969–974
Kececioglu J, Lenhof H, Mehlhorn K, Mutzel P, Reinert K, Vingron M (2000) A polyhedral approach to sequence alignment problems. Discret Appl Math 104:143–186
Kim J, Pramanik S, Chung MJ (1994) Multiple sequence alignment using simulated annealing. Bioinf 10(4):419–426
Kimura M (1980) A simple method for estimating evolutionary of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Klotz L, Blanken R (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91(2):261–272
Korostensky C, Gonnet GH (1999) Near optimal multiple sequence alignments using a traveling salesman problem approach. In: Proceedings of the String Processing and Information Retrieval Symposium. IEEE, Cancun, pp 105–114
Korostensky C, Gonnet GH (2000) Using traveling salesman problem algorithms for evolutionary tree construction. Bioinf 16(7):619–627
Krogh A, Brown M, Mian IS, Sjolander K, Haussler D (1994) Hidden markov models in computational biology: Applications to protein modeling. J Mol Biol 235:1501–1531
Kumar S, Tamura K, Nei M (1994) MEGA: Molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci 10:189–191
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5(2):150–163
Lawrence C, Altschul S, Boguski M, Liu J, Neuwald A, Wootton J (1993) Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment. Science 262:208–214
Lee EK, Easton T, Gupta K (2006) Novel evolutionary models and applications to sequence alignment problems. Annals Oper Res 148(1):167–187
Levenshtein VL (1966) Binary codes capable of correcting deletions, insertions, and reversals. Cybern Control Theor 10(9):707–710
Li W (1981) Simple method for constructing phylogenetic trees from distance matrices. Proc Natl Acad Sci USA 78(2):1085–1089
Lipman D, Altschul S, Kececioglu J (1989) A tool for multiple sequence alignment. Proc Natl Acad Sci USA 86(12):4412–4415
Maier D, Storer JA (1977) A note on the complexity of the superstring problem. Technical Report 233, Princeton University, USA
Nei M (1996) Phylogenetic analysis in molecular evolutionary genetics. Annu Rev Genet 30:371–403
Notredame C (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenomics 3(1):131–144
Notredame C, Higgins D (1996) SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res 24(8):1515–1524
Phillips A, Janies D, Wheeler W (2000) Multiple sequence alignment in phylogenetic analysis. Mol Phylogenet Evol 16(3):317–330
Piontkivska H (2004) Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used. Mol Phylogenet Evol 31(3):865–873
Purdom P, Bradford PG, Tamura K, Kumar S (2000) Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformamtics 16:140–151
Reinert K, Lenhof H, Mutzel P, Mehlhorn K, Kececioglu J (1997) A branch-and-cut algorithm for multiple sequence alignment. In: Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB-97). ACM Press, Santa Fe, pp 241–249
Ronquist F (1998) Fast fitch-parsimony algorithms for large data sets. Cladistics 14:387–400
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sankoff D, Cedergren RJ (1983) Simultaneous comparison of three or more sequences related by a tree. In: Sankoff D, Kruskal JB (eds) Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, MA, USA, pp 253–264
Shyu SJ, Tsai YT, Lee R (2004) The minimal spanning tree preservation approaches for DNA multiple sequence alignment and evolutionary tree construction. J Comb Optim 8(4):453–468
Sokal R, Michener C (1958) A statistical method for evaluating systematic relationships. University of Kansas, Scientific Bull 38:1409–1438
Stamatakis A, Ott M, Ludwig T (2005) RAxML-OMP: An efficient program for phylogenetic inference on SMPs. Lect Notes Comput Sci 3606:288–302
Swofford DL, Maddison WP (1987) Reconstructing ancestral character states under wagner parsimony. Math Biosci 87:199–229
Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz G (eds) Molecular Systs. Sinauer Associates, MA, USA, pp 411–501
Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1(3):269–85
Tajima F, Takezaki N (1994) Estimation of evolutionary distance for reconstructing molecular phylogenetic trees. Mol Biol Evol 11:278–286
Takahashi K, Nei M (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680
Vingron M, Haeseler A (1997) Towards integration of multiple alignment and phylogenetic tree construction. J Comput Biol 4(1):23–34
Vingron M, Waterman M (1994) Sequence alignment and penalty choice. review of concepts, case studies and implications. J Mol Biol 235(1):1–12
Wallace IM, O'Sullivan O, Higgins DG (2005) Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics 21(8):1408–14
Waterman M, Perlwitz M (1984) Line geometries for sequence comparisons. Bull Math Biol 46(4):567–577
Waterman MS (1995) Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman and Hall
Whelan S, Lio P, Goldman N (2001) Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 17(5):262–272
Yang Z (1993) Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10(6):1396–401
Zhang Y, Waterman M (2003) An eulerian path approach to global multiple alignment for DNA sequences. J Comput Biol 10(6):803–819
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Lee, E.K., Gupta, K. (2008). Algorithms for Genomic Analysis . In: Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74759-0_9
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