Development and Optimization of Integrated Pipelines for Phylogeny and Evolutionary Analyses

GUOQING, LU and SANTOSH, SERVISETTI and ZHENGXIN, CHEN (2014) Development and Optimization of Integrated Pipelines for Phylogeny and Evolutionary Analyses. In: International Conference on Advances in Environmental and Bio-Technology - AEBT 2014, 04-05 January, 2014, Bangkok.

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Abstract

Recently development of automated and integrated pipelines for phylogeny and evolutionary analyses has received a lot of attention. In this paper, we describe our approach of pipeline development. Our design focuses on integration, not only in the integrated result (i.e., the pipelines), but also in the integrated approach in the design process, so that we can exploit all kinds of resources available to us. In addition, we want integrated pipelines not only work effectively, but also efficiently. In this paper, we describe our two-step design: A basic approach and an optimized approach which takes advantage of parallelism offered by supercomputers. We present the major phases of pipeline development, describe methods used in optimization(including the sequence-split-logic), show the experimental result, and compare it with non-optimized implementation.

Item Type: Conference or Workshop Item (Paper)
Uncontrolled Keywords: Integrated pipelines, phylogeny, evolutionary analyses, parallelism, supercomputer, optimization
Depositing User: Mr. John Steve
Date Deposited: 11 May 2019 08:00
Last Modified: 11 May 2019 08:00
URI: http://publications.theired.org/id/eprint/2175

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