A faster algorithm for finding the minimum cut in a directed graph
SODA selected papers from the third annual ACM-SIAM symposium on Discrete algorithms
A supertree method for rooted trees
Discrete Applied Mathematics
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Incomplete Directed Perfect Phylogeny
SIAM Journal on Computing
Minimum-Flip Supertrees: Complexity and Algorithms
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bioinformatics
Bioinformatics
Exact ILP solutions for phylogenetic minimum flip problems
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Polynomial supertree methods revisited
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
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In computational phylogenetics, supertree methods provide a way to reconstruct larger clades of the Tree of Life. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. In particular, there exist methods based on encoding the input trees in a matrix, and methods based on finding minimum cuts in some graph. Matrix representation methods compute supertrees of superior quality, but the underlying optimization problems are computationally hard. In contrast, graph-based methods have polynomial running time, but supertrees are inferior in quality. In this paper, we present a novel approach for the computation of supertrees called FlipCut supertree. Our method combines the computation of minimum cuts from graph-based methods with a matrix representation method, namely Minimum Flip Supertrees. Here, the input trees are encoded in a 0/1/?-matrix. We present a heuristic to search for a minimum set of 0/1-flips such that the resulting matrix admits a directed perfect phylogeny. We then extend our approach by using edge weights to weight the columns of the 0/1/?-matrix. In our evaluation, we show that our method is extremely swift in practice, and orders of magnitude faster than the runner up. Concerning supertree quality, our method is sometimes on par with the "gold standard" Matrix Representation with Parsimony.