LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
On contract-and-refine transformations between phylogenetic trees
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Constructing large conservative supertrees
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
A robinson-foulds measure to compare unrooted trees with rooted trees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Algorithms for knowledge-enhanced supertrees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing rooted and unrooted RF supertrees is NP-hard. Nevertheless, effective local search heuristics have been developed for the restricted case where the input trees and the supertree are rooted.We describe new heuristics, based on the Edge Contract and Refine (ECR) operation, that remove this restriction, thereby expanding the utility of RF supertrees. We demonstrate that our local search algorithms yield supertrees with notably better scores than those obtained from rooted heuristics.