Regular Article: Extension Operations on Sets of Leaf-Labeled Trees
Advances in Applied Mathematics
Fixed-parameter tractability of graph modification problems for hereditary properties
Information Processing Letters
Reconstruction of rooted trees from subtrees
Discrete Applied Mathematics
Computing the local consensus of trees
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
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)
Exact ILP solutions for phylogenetic minimum flip problems
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Survey: A survey of the algorithmic aspects of modular decomposition
Computer Science Review
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In computational phylogenetics, the problem of constructinga consensus tree for a given set of input trees has frequently been addressed.In this paper we study the Minimum-Flip Problem: the inputtrees are transformed into a binary matrix, and we want to find a perfectphylogeny for this matrix using a minimum number of flips, that is,corrections of single entries in the matrix. In its graph-theoretical formulation,the problem is as follows: Given a bipartite graph G = (Vt∪Vc, E),the problem is to find a minimum set of edge modifications such that theresulting graph has no induced path with four edges which starts andends in Vt. We present a fixed-parameter algorithm for the Minimum-Flip Problemwith running time O(4.83k (m+n)+mn) for n taxa, m characters,and k flips. Additionally, we discuss several heuristic improvements. Wealso report computational results on phylogenetic data.