A generic arc-consistency algorithm and its specializations
Artificial Intelligence
A filtering algorithm for constraints of difference in CSPs
AAAI '94 Proceedings of the twelfth national conference on Artificial intelligence (vol. 1)
Tractable constraints on ordered domains
Artificial Intelligence
Regular Article: Extension Operations on Sets of Leaf-Labeled Trees
Advances in Applied Mathematics
Reconstruction of rooted trees from subtrees
Discrete Applied Mathematics
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A supertree method for rooted trees
Discrete Applied Mathematics
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Handbook of Constraint Programming (Foundations of Artificial Intelligence)
Handbook of Constraint Programming (Foundations of Artificial Intelligence)
Quartet-Based Phylogeny Reconstruction with Answer Set Programming
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
QUICKXPLAIN: preferred explanations and relaxations for over-constrained problems
AAAI'04 Proceedings of the 19th national conference on Artifical intelligence
Refining the basic constraint propagation algorithm
IJCAI'01 Proceedings of the 17th international joint conference on Artificial intelligence - Volume 1
Making AC-3 an optimal algorithm
IJCAI'01 Proceedings of the 17th international joint conference on Artificial intelligence - Volume 1
Implementing logical connectives in constraint programming
Artificial Intelligence
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A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called supertrees, whilst respecting the relationships in the original trees. A rooted tree exhibits an ultrametric property; that is, for any three leaves of the tree it must be that one pair has a deeper most recent common ancestor than the other pairs, or that all three have the same most recent common ancestor. This inspires a constraint programming encoding for rooted trees. We present an efficient constraint that enforces the ultrametric property over a symmetric array of constrained integer variables, with the inevitable property that the lower bounds of any three variables are mutually supportive. We show that this allows an efficient constraint-based solution to the supertree construction problem. We demonstrate that the versatility of constraint programming can be exploited to allow solutions to variants of the supertree construction problem.