Guided self-scheduling: A practical scheduling scheme for parallel supercomputers
IEEE Transactions on Computers
Aligning sequences via an evolutionary tree: complexity and approximation
STOC '94 Proceedings of the twenty-sixth annual ACM symposium on Theory of computing
A scalable content-addressable network
Proceedings of the 2001 conference on Applications, technologies, architectures, and protocols for computer communications
Popularity-Aware Greedy Dual-Size Web Proxy Caching Algorithms
ICDCS '00 Proceedings of the The 20th International Conference on Distributed Computing Systems ( ICDCS 2000)
A component-based implementation of multiple sequence alignment
Proceedings of the 2003 ACM symposium on Applied computing
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Multiple sequence alignment (MSA) and phylogenetic tree reconstruction are one of the most important problems in the computational biology. While both these problems are of great practical significance, in most cases they are very computationally demanding. In this paper we propose a new approach to the MSA problem which simultaneously infers an underlying phylogenetic tree. To process large data sets we provide parallel implementation of our method, which is based on the distributed caching of intermediate results. Finally, we show a parallel server designed for grid environments, and we report results of experiments performed with actual biological data, e.g. 1000 ribosomal RNA sequences.