FPGA acceleration of the phylogenetic parsimony kernel?

Nikolaos Alachiotis; Alexandros Stamatakis

doi:10.1109/FPL.2011.83

FPGA acceleration of the phylogenetic parsimony kernel?

Nikolaos Alachiotis^*, Alexandros Stamatakis

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

18 Citations (Scopus)

Abstract

The phylogenetic parsimony function is a popular, discrete criterion for reconstructing evolutionary trees based on molecular sequence data. Parsimony strives to find the phylogenetic tree that explains the evolutionary history of organisms by the least number of mutations. Because parsimony is a discrete function, it should fit well to FPGAs. We present a versatile FPGA implementation of the parsimony function and compare its performance to a highly optimized SSE3- and AVX-vectorized software implementation.We find that, because of a particular constellation in our lab, the speedups that can be achieved by using an FPGA, are substantially less impressive, than usually reported in papers on FPGA acceleration of bioinformatics kernels.We conclude that, a competitive spirit between SW and HW application developers can contribute toward obtaining more objective performance comparisons.

Original language	English
Title of host publication	Proceedings - 21st International Conference on Field Programmable Logic and Applications, FPL 2011
Place of Publication	Piscataway, NJ
Publisher	IEEE
Pages	417-422
Number of pages	6
ISBN (Electronic)	978-0-7695-4529-5
ISBN (Print)	978-1-4577-1484-9
DOIs	https://doi.org/10.1109/FPL.2011.83
Publication status	Published - 13 Oct 2011
Externally published	Yes
Event	21st International Conference on Field Programmable Logic and Applications, FPL 2011 - Chania, Greece Duration: 5 Sept 2011 → 7 Sept 2011 Conference number: 21

Publication series

Name	Proceedings - International Conference on Field Programmable Logic and Applications (FPL)
Publisher	IEEE
Volume	2011
ISSN (Print)	1946-147X
ISSN (Electronic)	1946-1488

Conference

Conference	21st International Conference on Field Programmable Logic and Applications, FPL 2011
Abbreviated title	FPL 2011
Country/Territory	Greece
City	Chania
Period	5/09/11 → 7/09/11

Keywords

FPGA
Parsimony
Performance analysis
SIMD

Access to Document

10.1109/FPL.2011.83

Cite this

Alachiotis, N., & Stamatakis, A. (2011). FPGA acceleration of the phylogenetic parsimony kernel? In Proceedings - 21st International Conference on Field Programmable Logic and Applications, FPL 2011 (pp. 417-422). Article 6044856 (Proceedings - International Conference on Field Programmable Logic and Applications (FPL); Vol. 2011). IEEE. https://doi.org/10.1109/FPL.2011.83

@inproceedings{02347ca189a14781877fe3e1653b4d08,

title = "FPGA acceleration of the phylogenetic parsimony kernel?",

abstract = "The phylogenetic parsimony function is a popular, discrete criterion for reconstructing evolutionary trees based on molecular sequence data. Parsimony strives to find the phylogenetic tree that explains the evolutionary history of organisms by the least number of mutations. Because parsimony is a discrete function, it should fit well to FPGAs. We present a versatile FPGA implementation of the parsimony function and compare its performance to a highly optimized SSE3- and AVX-vectorized software implementation.We find that, because of a particular constellation in our lab, the speedups that can be achieved by using an FPGA, are substantially less impressive, than usually reported in papers on FPGA acceleration of bioinformatics kernels.We conclude that, a competitive spirit between SW and HW application developers can contribute toward obtaining more objective performance comparisons.",

keywords = "FPGA, Parsimony, Performance analysis, SIMD",

author = "Nikolaos Alachiotis and Alexandros Stamatakis",

year = "2011",

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doi = "10.1109/FPL.2011.83",

language = "English",

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booktitle = "Proceedings - 21st International Conference on Field Programmable Logic and Applications, FPL 2011",

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note = "21st International Conference on Field Programmable Logic and Applications, FPL 2011, FPL 2011 ; Conference date: 05-09-2011 Through 07-09-2011",

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Alachiotis, N & Stamatakis, A 2011, FPGA acceleration of the phylogenetic parsimony kernel? in Proceedings - 21st International Conference on Field Programmable Logic and Applications, FPL 2011., 6044856, Proceedings - International Conference on Field Programmable Logic and Applications (FPL), vol. 2011, IEEE, Piscataway, NJ, pp. 417-422, 21st International Conference on Field Programmable Logic and Applications, FPL 2011, Chania, Greece, 5/09/11. https://doi.org/10.1109/FPL.2011.83

FPGA acceleration of the phylogenetic parsimony kernel? / Alachiotis, Nikolaos; Stamatakis, Alexandros.
Proceedings - 21st International Conference on Field Programmable Logic and Applications, FPL 2011. Piscataway, NJ: IEEE, 2011. p. 417-422 6044856 (Proceedings - International Conference on Field Programmable Logic and Applications (FPL); Vol. 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review