Journal
IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS
Volume E100D, Issue 2, Pages 256-264Publisher
IEICE-INST ELECTRONICS INFORMATION COMMUNICATIONS ENG
DOI: 10.1587/transinf.2015EDP7433
Keywords
FPGA; hardware acceleration; phylogenetic tree reconstruction; maximum parsimony
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In this paper, we present an FPGA hardware implementation for a phylogenetic tree reconstruction with a maximum parsimony algorithm. We base our approach on a particular stochastic local search algorithm that uses the Progressive Neighborhood and the Indirect Calculation of Tree Lengths method. This method is widely used for the acceleration of the phylogenetic tree reconstruction algorithm in software. In our implementation, we define a tree structure and accelerate the search by parallel and pipeline processing. We show results for eight real-world biological datasets. We compare execution times against our previous hardware approach, and TNT, the fastest available parsimony program, which is also accelerated by the Indirect Calculation of Tree Lengths method. Acceleration rates between 34 to 45 per rearrangement, and 2 to 6 for the whole search, are obtained against our previous hardware approach. Acceleration rates between 2 to 36 per rearrangement, and 18 to 112 for the whole search, are obtained against TNT.
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