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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)
Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner.(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)
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)
MOTIVATION The advent of next-generation sequencing technologies has increased the accuracy and quantity of sequence data, opening the door to greater opportunities in genomic research. RESULTS In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable of overcoming two major obstacles in the mapping of reads from(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)