Hyrum Carroll

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MOTIVATION Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively(More)
— Phylogenetic analysis is an integral part of biological research. As the number of sequenced genomes increases, available data sets are growing in number and size. Several algorithms have been proposed to handle these larger data sets. A family of algorithms known as disc covering methods (DCMs), have been selected by the NSF funded CIPRes project to(More)
—The performance of maximum likelihood searches can be boosted by using the most parsimonious tree as a starting point for the search. The time spent in performing the parsimony search to find this starting tree is insignificant compared to the time spent in the maximum likelihood search, leading to an overall gain in search time. These parsimony boosted(More)
PSODA is a comprehensive phylogenetics package, including alignment, phylogenetic search under both parsimony and maximum likelihood, and visualisation and analysis tools. PSODA offers performance comparable to PAUP* in an open source package that aims to provide a foundation for researchers examining new phylogenetic algorithms. A key new feature is(More)
—Due to the immensity of phylogenetic tree space for large data sets, researches must rely on heuristic searches to infer reasonable phylogenies. By designing meta-searches which appropriately combine a variety of heuristics and parameter settings, researchers can significantly improve the performance of heuristic searches. Advanced language constructs in(More)
DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach , has been shown to be effective in combining alignment and phylogenetic(More)
This thesis has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory. As chair of the candidate's graduate committee, I have read the thesis of Hyrum D. Carroll in its final form and have found that (1) its format, citations, and bibliographical style are consistent and acceptable and fulfill(More)
The relationship between changes in gene expression and physical characteristics associated with Down syndrome is not well understood. Chromosome 21 genes interact with nonchromosome 21 genes to produce Down syndrome characteristics. This indirect influence, however, is difficult to empirically define due to the number, size, and complexity of the involved(More)