Two strikes against perfect phylogeny
 Hans L. Bodlaender,
 Mike R. Fellows,
 Tandy J. Warnow
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Abstract
One of the major efforts in molecular biology is the computation of phytogenies for species sets. A longstanding open problem in this area is called the Perfect Phylogeny problem. For almost two decades the complexity of this problem remained open, with progress limited to polynomial time algorithms for a few special cases, and many relaxations of the problem shown to be NPComplete. From an applications point of view, the problem is of interest both in its general form, where the number of characters may vary, and in its fixedparameter form. The Perfect Phylogeny problem has been shown to be equivalent to the problem of triangulating colored graphs[30]. It has also been shown recently that for a given fixed number of characters the yesinstances have bounded treewidth[45], opening the possibility of applying methodologies for bounded treewidth to the fixedparameter form of the problem. We show that the Perfect Phylogeny problem is difficult in two different ways. We show that the general problem is NPComplete, and we show that the various finitestate approaches for bounded treewidth cannot be applied to the fixedparameter forms of the problem.
 Title
 Two strikes against perfect phylogeny
 Book Title
 Automata, Languages and Programming
 Book Subtitle
 19th International Colloquium Wien, Austria, July 13–17, 1992 Proceedings
 Pages
 pp 273283
 Copyright
 1992
 DOI
 10.1007/3540557199_80
 Print ISBN
 9783540557197
 Online ISBN
 9783540472780
 Series Title
 Lecture Notes in Computer Science
 Series Volume
 623
 Series ISSN
 03029743
 Publisher
 Springer Berlin Heidelberg
 Copyright Holder
 SpringerVerlag
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 Editors
 Authors

 Hans L. Bodlaender ^{(1)}
 Mike R. Fellows ^{(2)}
 Tandy J. Warnow ^{(3)}
 Author Affiliations

 1. Department of Computer Science, P.O. Box 80.089, 3508, TB Utrecht, the Netherlands
 2. Computer Science Department, University of Victoria, Victoria, B.C., Canada
 3. Department of Mathematics, University of Southern California, Los Angeles, California, USA
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