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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)
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)
While there is growing interest in using Java for high-performance applications, many in the high-performance computing community do not believe that Java can match the performance of traditional native message passing environments. This paper discusses critical issues that must be addressed in the design of Java based message passing systems. EEcient(More)
As the Internet began its exponential growth into a global information environment, software was often unreliable, slow and had dif£culty in interoperating with other systems. Supercomputing node counts also continue to follow high growth trends. Supercomputer and grid resource management software must mature into a reliable computational platform in much(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)