Paper Info
Title
The Complexity of Phylogeny Constraint Satisfaction.
Abstract
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet consistency problem, and many other problems studied in the bioinformatics literature. The studied problems can be described as constraint satisfaction problems where the constraints have a first-order definition over the rooted triple relation. We show that every such phylogeny problem can be solved in polynomial time or is NP-complete. On the algorithmic side, we generalize a well-known polynomial-time algorithm of Aho, Sagiv, Szymanski, and Ullman for the rooted triple consistency problem. Our algorithm repeatedly solves linear equation systems to construct a solution in polynomial time. We then show that every phylogeny problem that cannot be solved by our algorithm is NP-complete. Our classification establishes a dichotomy for a large class of infinite structures that we believe is of independent interest in universal algebra, model theory, and topology. The proof of our main result combines results and techniques from various research areas: a recent classification of the model-complete cores of the reducts of the homogeneous binary branching C-relation, Leeb's Ramsey theorem for rooted trees, and universal algebra.
Year
DOI
Venue
2015
10.4230/LIPIcs.STACS.2016.20
Leibniz International Proceedings in Informatics
Keywords
DocType
Volume
constraint satisfaction problems,computational complexity,phylogenetic reconstruction,Ramsey theory,model theory
Journal
47
ISSN
Citations 
PageRank 
1868-8969
6
0.47
References 
Authors
12
3
Name
Order
Citations
PageRank
Manuel Bodirsky164454.63
Peter Jonsson2101.59
trung van pham3285.02