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This paper presents the design of NetPIPE, a new Network Protocol Independent Performance Evaluator. NetPIPE maps the performance of a network across a wide range and presents the data in a new manner. Its protocol independence allows for visualization of the overhead associated with a protocol layer. Using Net-PIPE has led to the discovery of a deep plunge(More)
Phylogentic analysis is becoming an increasingly important tool for customized drug treatments, epidemiological studies, and evolutionary analysis. The TCS method provides an important tool for dealing with genes at a population level. Existing software for TCS analysis takes an unreasonable amount of time for the analysis of significant numbers of Taxa.(More)
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)
Recent advances in DNA sequencing technology have created large data sets upon which phylogenetic inference can be performed. However, current research is limited by the prohibitive time necessary to perform tree search on even a reasonably-sized data set. Some parallel algorithms have been developed but the biological research community does not use them(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)
Phylogenetic analysis is a central tool in studies of comparative genomics. When a new region of DNA is isolated and sequenced, researchers are often forced to throw away months of computation on an existing phylogeny of homologous sequences in order to incorporate this new sequence. The previously constructed trees are often discarded, and the researcher(More)