A tabu search algorithm for maximum parsimony phylogeny inference

European Journal of Operational Research

Volumn 176, Issue 3, 2007, Pages 1908-1917

  Lin, Yu Min ^a   Fang, Shu Cherng ^a,c   Thorne, Jeffrey L ^b  

^a North Carolina State University   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c TSINGHUA UNIVERSITY   (China)

Author keywords

Bioinformatics; Maximum parsimony; OR in biology; Phylogeny inference; Tabu search

Indexed keywords

BIOINFORMATICS; MAXIMUM PARSIMONY; PHYLOGENY INFERENCE; TABU SEARCH;

ALGORITHMS; COMBINATORIAL MATHEMATICS; OPTIMIZATION; PROBLEM SOLVING; TREES (MATHEMATICS);

OPERATIONS RESEARCH;

EID: 33750030429     PISSN: 03772217     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejor.2005.10.031     Document Type: Article

References (28)

1. J. Błażewicz, P. Formanowicz, F. Glover, M. Kasprzak, J. We{ogonek}glarz, An improved tabu search algorithm for DNA sequencing with errors, in: Proceedings of the III Meta-heuristics International Conference, Angra dos Reis, 1999, pp. 69-75.
2. Brauer M.J., Holder M.T., Dries L.A., Zwickl D.J., Lewis P.O., and Hillis D.M. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Molecular Biology and Evolution 19 (2002) 1717-1726
3. Congdon C.B. Gaphyl: A genetic algorithms approach to cladistics. In: DeRaedt L., and Siebes A. (Eds). Principles of Data Mining and Knowledge Discovery. Lecture Notes in Computer Science vol. 2168 (2001), Springer-Verlag, Berlin 67-78
4. Durbin R., Eddy S., Krogh A., and Mitchison G. Building Phylogenetic Trees. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1998), Cambridge University Press, Cambridge, UK pp. 160-191
5. Edwards A.W.F., and Cavalli-Sforza L.L. The reconstruction of evolution. Annals of Human Genetics 27 (1963) 105-106
6. A.W.F. Edwards, L.L. Cavalli-Sforza, Reconstruction of evolutionary trees, in: V.H. Heywood, J. McNeill (Eds,), Phenetic and Phylogenetic Classification, Systematics Association Publish, No. 6, London, 1964, pp. 67-76.
7. J. Felsenstein, PHYLIP (phylogeny inference package), Version 3.57c. Distributed by the author, Department of Genetics, University of Washington, Seattle, 1995.
8. Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates, Boston, MA
9. Fitch W.M. Toward defining the course of evolution: Minimum change for a specified tree topology. Systematic Zoology 20 (1971) 406-416
10. Fitch W.M. On the problem of discovering the most parsimonious tree. American Naturalist 111 (1997) 223-255
11. Glover F. Tabu search-Part I. ORSA Journal on Computing 1 (1989) 190-206
12. Gendreau M., Laporte G., and Séguin R. A tabu search heuristic for the vehicle routing problem with stochastic demands and customers. Operations Research 44 (1996) 469-477
13. Gernandt D.S., and Stone J.K. Phylogenetic analysis of nuclear ribosomal DNA places the nematode parasite, Drechmeria coniospora, in Clavicipitaceae. Mycologia 91 (1999) 993-1000
14. Goloboff P.A. Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15 (1999) 415-428
15. Graham R.L., and Foulds L.R. Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time. Mathematical Biosciences 60 (1982) 133-142
16. Hendy M.D., and Penny D. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59 (1982) 277-290
17. Kluge A.G., and Farris J.S. Quantitative phyletics and the evolution of anurans. Systematic Zoology 18 (1969) 1-32
18. Kuhner M.K., and Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11 (1994) 459-468
19. Lewis P.O. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Molecular Biology and Evolution 15 (1998) 277-283
20. Li W.H. Molecular Evolution (1997), Sinauer Associates, Boston, MA
21. Lundy M. Applications of the annealing algorithm to combinatorial problems in statistics. Biometrika 72 (1985) 191-198
22. H. Matsuda, Protein phylogenetic inference using maximum likelihood with a genetic algorithm, in: Pacific Symposium on Biocomputing, 1996, pp. 512-523.
23. Mau B., Newton M.A., and Larget B. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55 (1999) 1-12
24. Robinson D.F., and Foulds L.R. Comparison of phylogenetic trees. Mathematical Biosciences 53 (1981) 131-147
25. Saitou N., and Nei M. The neighbor-joining method: A new method for reconstruction phylogenetic trees. Molecular Biology and Evolution 4 (1987) 406-425
26. *: Phylogenetic Analysis using Parsimony (*and Other Methods) (2000), Sinauer Associates, Sunderland, Mass
27. Zachariasen M., and Dam M. Tabu search on the geometric traveling salesman problem. In: Osman I.H., and Kelly J.P. (Eds). Meta-heuristics: Theory and Applications (1996), Kluwer Academic Publishers, Boston 571-587
28. Zuckerkandl E., and Pauling L. Molecular disease evolution and genetic heterogeneity. In: Marsha M., and Pullman B. (Eds). Horizons in Biochemistry (1962), Academic Press 189-225