Improved Approximation Algorithms for Tree Alignment

Journal of Algorithms

Volumn 25, Issue 2, 1997, Pages 255-273

  Wang, Lusheng ^a   Gusfield, Dan ^b  

^a CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^b University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000503180     PISSN: 01966774     EISSN: None     Source Type: Journal    
DOI: 10.1006/jagm.1997.0882     Document Type: Article

References (14)

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3. S. K. Gupta, J. D. Kececioglu, and A. A. Schaffer, Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice, in "Combinatorial Pattern Matching 95," pp. 128-143.
4. D. Gusfield, Efficient methods for multiple sequence alignment with guaranteed error bounds, Bull. Math. Biol. 55 (1993), 141-154.
5. J. J. Hein, 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 (1989), 649-668.
6. D. J. Lipman, S. F. Altschul, and J. D. Kececioglu, A tool for multiple sequence alignment, Proc. Nat. Acad. Sci. U.S.A. 86 (1989), 4412-4415.
7. R. Ravi and J. Kececioglu, Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree, in "Combinatorial Pattern Matching 95," pp. 330-339.
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9. D. Sankoff and R. Cedergren, Simultaneous comparisons of three or more sequences related by a tree, in "Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison" (D. Sankoff and J. Kruskal, Eds.), pp. 253-264, Addison-Wesley, Reading, MA, 1983.
10. D. Sankoff, R. J. Cedergren, and G. Lapalme, Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA, J. Mol. Evol. 7 (1976), 133-149.
11. D. Sankoff and J. Kruskal, "Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison," Addison-Wesley, Reading, MA, 1983.
12. L. Wang and T. Jiang, On the complexity of multiple sequence alignment, J. Comput. Biol. 1 (1994), 337-348.
13. L Wang, T. Jiang, and E. L. Lawler, Approximation algorithms for tree alignment with a given phylogeny, Algorithmic 16 (1996), 302-315.
14. M. S. Waterman and M. D. Perlwitz, Line geometries for sequence comparisons, Bull. Math. Biol. 46 (1984), 567-577.