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)
Heterogeneous computing environments are becoming an increasingly popular platform for executing parallel applications. Such environments consist of a diverse set of machines and o er considerably more computational power at a lower cost than a parallel computer. E cient heterogeneous parallel applications must account for the di erences inherent in such an(More)
Consensus trees are a popular approach for summarizing the shared evolutionary relationships in a collection of trees. Many popular techniques such as Bayesian analyses produce results that can contain tens of thousands of trees to summarize. We develop a fast consensus algorithm called HashCS to construct large-scale consensus trees. We perform an(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)
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 to(More)
For centuries, the research paper have been the main vehicle for scientific progress. From the paper, readers in the scientific community are expected to extract all the relevant information necessary to reproduce and validate the results presented by the paper’s authors. However, the increased use of computer software in science makes reproducing(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)
Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as(More)