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Multiple sequence alignment


References:

[1] - S. K. Gupta, J. D. Kececioglu, A. A. Schäffer
      Improving the Practical Space and Time Efficiency 
      of the Shortest-Paths Approach 
      to Sum-of-Pairs Multiple Sequence Alignment
      Proc. 6th Annual Combinatorial Pattern Matching 
      conference (CPM '95)

[2] - J. Stoye 
      Multiple sequence alignment 
      with the divide-and-conquer method (1998) 
      Gene, 211 (2), GC45-GC56. 

[3] - Gribskov, M., McLachlan, A.D., and Eisenberg, D. 
      Profile analysis: detection of distantly related proteins 
      Proceedings of the National Academy of Sciences, 
      84,4355-4358, 1987. 

[4] - Higgins,D.G. and Sharp,P.M. (1988) 
      CLUSTAL: a package for performing multiple
      sequence alignment on a microcomputer. 
      Gene 73,237-244.

[5] - B. Morgenstern, A. Dress, T. Werner (1996) 
      Multiple DNA and protein sequence alignment 
      based on segment-to-segment comparison.
      Proc. Natl. Acad. Sci. USA 93, 12098 - 12103. 

[6] - Sneath & Sokal 1973
      Numerical Taxonomy 
      Freeman, San Francisco

[7] -  David Sankoff and Robert J. Cedergren
       Simultaneous Comparison of Three or More Sequences
       Related by a Tree
       In "An Overview of Sequence Comparison" J. Kruskal, 
       ed. David Sankoff and Joseph B. Kruskal,
       ch. 9, p. 253--263,

[8] - Jotun 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, p. 649--668, (1989)

[9] - Schikowski, B. and Vingron, M. (1997) 
      A Clustering Approach to Generalized Tree Alignment 
      with Application to Alu Repeats
      Proceedings of the German Conference on Bioinformatics GCB '96. 
      Lecture Notes in Computer Science, Springer-Verlag, 1997, pp 47--55 

[10] - Tao Jiang and Eugene L. Lawler and Lusheng Wang
       Aligning Sequences via an Evolutionary Tree:
       Complexity and Approximation (Extended Abstract)
       in Proceedings of the Twenty-Sixth Annual {ACM} Symposium
       on Theory of Computing
       p. 760--769 (1994)



Comments are very welcome.
luz@molgen.mpg.de