%0 Journal Article
%T Robinson-Foulds Supertrees
%A Mukul S Bansal
%A J Gordon Burleigh
%A Oliver Eulenstein
%A David Fern¨¢ndez-Baca
%J Algorithms for Molecular Biology
%D 2010
%I BioMed Central
%R 10.1186/1748-7188-5-18
%X We introduce efficient, local search based, hill-climbing heuristics for the intrinsically hard RF supertree problem on rooted trees. These heuristics use novel non-trivial algorithms for the SPR and TBR local search problems which improve on the time complexity of the best known (na£¿ve) solutions by a factor of ¦¨(n) and ¦¨(n2) respectively (where n is the number of taxa, or leaves, in the supertree). We use an implementation of our new algorithms to examine the performance of the RF supertree method and compare it to matrix representation with parsimony (MRP) and the triplet supertree method using four supertree data sets. Not only did our RF heuristic provide fast estimates of RF supertrees in all data sets, but the RF supertrees also retained more of the information from the input trees (based on the RF distance) than the other supertree methods.Our heuristics for the RF supertree problem, based on our new local search algorithms, make it possible for the first time to estimate large supertrees by directly optimizing the RF distance from rooted input trees to the supertrees. This provides a new and fast method to build accurate supertrees. RF supertrees may also be useful for estimating majority-rule(-) supertrees, which are a generalization of majority-rule consensus trees.Supertree methods provide a formal approach for combining small phylogenetic trees with incomplete species overlap in order to build comprehensive species phylogenies, or supertrees, that contain all species found in the input trees. Supertree analyses have produced the first family-level phylogeny of flowering plants [1] and the first phylogeny of nearly all extant mammal species [2]. They have also enabled phylogenetic analyses using large-scale genomic data sets in bacteria, across eukaryotes, and within plants [3,4] and have helped elucidate the origin of eukaryotic genomes [5]. Furthermore, supertrees have been used to examine rates and patterns of species diversification [1,2], to test hy
%U http://www.almob.org/content/5/1/18