Reconstruction of rooted trees from subtrees
Discrete Applied Mathematics
Computing the Local Consensus of Trees
SIAM Journal on Computing
A supertree method for rooted trees
Discrete Applied Mathematics
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
Minimum-Flip Supertrees: Complexity and Algorithms
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An improved fixed-parameter algorithm for minimum-flip consensus trees
IWPEC'08 Proceedings of the 3rd international conference on Parameterized and exact computation
FlipCut supertrees: towards matrix representation accuracy in polynomial time
COCOON'11 Proceedings of the 17th annual international conference on Computing and combinatorics
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In computational phylogenetics, the problem of constructing a consensus tree or supertree of a given set of rooted input trees can be formalized in different ways. We consider the Minimum Flip Consensus Tree and Minimum Flip Supertree problem, where input trees are transformed into a 0/1/?-matrix, such that each row represents a taxon, and each column represents a subtree membership. For the consensus tree problem, all input trees contain the same set of taxa, and no ?-entries occur. For the supertree problem, the input trees may contain different subsets of the taxa, and unrepresented taxa are coded with ?-entries. In both cases, the goal is to find a perfect phylogeny for the input matrix requiring a minimum number of 0/1-flips, i.e., matrix entry corrections. Both optimization problems are NP-hard. We present the first efficient Integer Linear Programming (ILP) formulations for both problems, using three distinct characterizations of a perfect phylogeny. Although these three formulations seem to differ considerably at first glance, we show that they are in fact polytope-wise equivalent. Introducing a novel column generation scheme, it turns out that the simplest, purely combinatorial formulation is the most efficient one in practice. Using our framework, it is possible to find exact solutions for instances with ~100 taxa.