Fast local search for unrooted Robinson-foulds supertrees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Identifying rogue taxa through reduced consensus: NP-Hardness and exact algorithms
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
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Generalizations of the strict and loose consensus methods to the supertree setting, recently introduced by McMorris and Wilkinson, are studied. The supertrees these methods produce are conservative in the sense that they only preserve information (in the form of splits) that is supported by at least one the input trees and that is not contradicted by any of the input trees. Alternative, equivalent, formulations of these supertrees are developed. These are used to prove the NP-completeness of the underlying optimization problems and to give exact integer linear programming solutions. For larger data sets, a divide and conquer approach is adopted, based on the structural properties of these supertrees. Experiments show that it is feasible to solve problems with several hundred taxa and several hundred trees in a reasonable amount of time.