Tiffani L. Williams

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Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a(More)
Phylogenetic trees are commonly reconstructed based on hard optimization problems such as maximum parsimony (MP) and maximum likelihood (ML). Conventional MP heuristics for producing phylogenetic trees produce good solutions within reasonable time on small datasets (up to a few thousand sequences), while ML heuristics are limited to smaller datasets (up to(More)
BACKGROUND MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework for designing phylogenetic applications. The problem of interest is generating the all-to-all Robinson-Foulds distance matrix, which has many(More)
Heterogeneous computing environments are becoming an increasingly popular platform for executing parallel applications. Such environments consist of a diverse set of machines and ooer considerably more computational power at a lower cost than a parallel computer. EEcient heterogeneous parallel applications must account for the diierences inherent in such an(More)
BACKGROUND Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores(More)
Large and comprehensive phylogenetic trees are desirable for studying macroevolutionary processes and for classification purposes. One approach for obtaining large phylogenies is to combine the topologies (or source trees) from previous phylogenetic studies. Tree reconstruction techniques that use the above methodology are known as supertree methods. In(More)
Many large-scale phylogenetic reconstruction methods attempt to solve hard optimization problems (such as Maximum Parsimony (MP) and Maximum Likelihood (ML)), but they are limited severely by the number of taxa that they can handle in a reasonable time frame. A standard heuristic approach to this problem is the divide-and-conquer strategy: decompose the(More)
In this paper, we study two fast algorithms—HashRF and PGM-Hashed—for computing the Robinson-Foulds (RF) distance matrix between a collection of evolutionary trees. The RF distance matrix represents a tremendous data-mining opportunity for helping biologists understand the evolutionary relationships depicted among their trees. The novelty of our work(More)
Phylogenetic analysis often produce a large number of candidate evolutionary trees, each a hypothesis of the " true " tree. Post-processing techniques such as strict consensus trees are widely used to summarize the evolutionary relationships into a single tree. However, valuable information is lost during the summarization process. A more elementary step is(More)