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- W2894698540 abstract "PhyML is one of the most widely used phylogenetic tree reconstruction programs. Phylogenetic bootstrapping is the classic technique to measure the reliability of a tree that consists of creating disturbances to the original alignment to generate replicates. PhyML 3.0 is an open source program that already includes the bootstrap technique, and this technique is furthermore parallelized in this version using MPI. The parallel solution is based on point-to-point communication operations that are produced within a loop with “number of replicates/number of processors” iterations, causing each processor to construct one phylogenetic tree at a time. The purpose of this work was to modify the parallel version in order to achieve better performance, by firstly replacing the point-to-point communication operations with collective communication operations, and secondly reducing the number of produced messages. The data sets used in the performance evaluation include both synthetic and real data also used by the programs PhyML, RaxML and fatsDNAml. Based on the performance analysis, it was verified that the proposed solution outperforms the original solution, thus proving that collective operations are more efficient than point-to-point operations, and that the grouping of iterations for each processor helps in the overall performance of the application. In addition, it was observed that the proposed solution increases its speedup as the number of bootstrap replicates increases, with a fixed number of processors." @default.
- W2894698540 created "2018-10-12" @default.
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- W2894698540 date "2018-01-01" @default.
- W2894698540 modified "2023-09-27" @default.
- W2894698540 title "Parallel Solution Based on Collective Communication Operations for Phylogenetic Bootstrapping in PhyML 3.0" @default.
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- W2894698540 doi "https://doi.org/10.1007/978-3-030-01722-4_13" @default.
- W2894698540 hasPublicationYear "2018" @default.
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