13 Result(s)
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Tiffani L. Williams
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Article
Open AccessFast algorithms for computing phylogenetic divergence time
The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet...
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Chapter and Conference Paper
A Fast Algorithm for Computing the Quartet Distance for Large Sets of Evolutionary Trees
We present the QuickQuartet algorithm for computing the all-to-all quartet distance for large evolutionary tree collections. By leveraging the relationship between bipartitions and quartets, our approach signi...
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Article
Open AccessAn efficient and extensible approach for compressing phylogenetic trees
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 tre...
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Article
Open AccessMrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees
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 fo...
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Chapter and Conference Paper
Large-Scale Analysis of Phylogenetic Search Behavior
Phylogenetic analysis is used in all branches of biology with applications ranging from studies on the origin of human populations to investigations of the transmission patterns of HIV. Most phylogenetic analy...
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Chapter and Conference Paper
A Novel Approach for Compressing Phylogenetic Trees
Phylogenetic trees are tree structures that depict relationships between organisms. Popular analysis techniques often produce large collections of candidate trees, which are expensive to store. We introduce Tr...
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Article
Open AccessUsing tree diversity to compare phylogenetic heuristics
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...
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Chapter and Conference Paper
An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections
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...
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Chapter and Conference Paper
A Fitness Distance Correlation Measure for Evolutionary Trees
Phylogenetics is concerned with inferring the genealogical relationships between a group of organisms (or taxa), and this relationship is usually expressed as an evolutionary tree. However, inferring the phylo...
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Chapter and Conference Paper
Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices
In this paper, we introduce the HashRF(p,q) algorithm for computing RF matrices of large binary, evolutionary tree collections. The novelty of our algorithm is that it can be used to compute arbitrarily-sized (p ...
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Chapter and Conference Paper
An Experimental Analysis of Robinson-Foulds Distance Matrix Algorithms
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 tremendo...
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Chapter
Performance of Supertree Methods on Various Data Set Decompositions
Many large-scale phylogenetic reconstruction methods attempt to solve hard optimization problems such as Maximum Parsimony (MP) and Maximum Likelihood (ML), but they are severely limited by the number of taxa ...
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Chapter and Conference Paper
The Heterogeneous Bulk Synchronous Parallel Model
Trends in parallel computing indicate that heterogeneous parallel computing will be one of the most widespread platforms for computation-intensive applications. A heterogeneous computing environment offers con...
