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)
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)
—We present a new algorithm, ChemAlign, that uses physicochemical properties and secondary structure elements to create biologically relevant multiple sequence alignments (MSAs). Additionally, we introduce the Physic-ochemical Property Difference (PPD) score for the evaluation of MSAs. This score is the normalized difference of physicochemical property(More)
—PSODA is an open-source phylogenetic search application that implements traditional parsimony and likelihood search techniques as well as advanced search algorithms. PSODA is compatible with PAUP and the search algorithms are competitive with those in PAUP. PSODA also adds a basic scripting language to the PAUP block, making it possible to easily create(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)
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)
— 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)
— Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well(More)
SUMMARY Many online sources of gene interaction networks supply rich visual data regarding gene pathways that can aid in the study of biological processes, disease research and drug discovery. PathGen incorporates data from several sources to create transitive connections that span multiple gene interaction databases. Results are displayed in a(More)
BACKGROUND Long branch attraction (LBA) is a problem that afflicts both the parsimony and maximum likelihood phylogenetic analysis techniques. Research has shown that parsimony is particularly vulnerable to inferring the wrong tree in Felsenstein topologies. The long branch extraction method is a procedure to detect a data set suffering from this problem so(More)