A generic and versatile architecture for inference of evolutionary trees under maximum likelihood

Nikolaos Alachiotis; Alexandros Stamatakis

doi:10.1109/ACSSC.2010.5757682

A generic and versatile architecture for inference of evolutionary trees under maximum likelihood

Nikolaos Alachiotis^*, Alexandros Stamatakis

^*Corresponding author for this work

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

2 Citations (Scopus)

Abstract

Likelihood-based reconstruction of phylogenetic (evolutionary) trees from molecular sequence data exhibits extreme resource requirements because of the high computational cost of the phylogenetic likelihood function. We propose a dedicated computer architecture for the inference of phylogenies under the maximum likelihood criterion. Our design is sufficiently generic to support any possible input data type, that is, DNA, RNA secondary structure, or protein data. Furthermore, the architecture is able to calculate log-likelihood scores and perform numerical scaling to maintain numerical stability on large datasets. It can also optimize the branch lengths of tree topologies and calculate transition probability matrices. We used FPGA technology to verify the correctness of our architecture.

Original language	English
Title of host publication	Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010
Place of Publication	Piscataway, NJ
Publisher	IEEE
Pages	829-835
Number of pages	7
ISBN (Electronic)	978-1-4244-9721-8
ISBN (Print)	978-1-4244-9722-5
DOIs	https://doi.org/10.1109/ACSSC.2010.5757682
Publication status	Published - 2010
Externally published	Yes
Event	44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010 - Pacific Grove, United States Duration: 7 Nov 2010 → 10 Nov 2010 Conference number: 44

Publication series

Name	Conference Record - Asilomar Conference on Signals, Systems and Computers
Publisher	IEEE
Volume	2010
ISSN (Print)	1058-6393
ISSN (Electronic)	1058-6393

Conference

Conference	44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010
Abbreviated title	Asilomar 2010
Country/Territory	United States
City	Pacific Grove
Period	7/11/10 → 10/11/10

Access to Document

10.1109/ACSSC.2010.5757682

Cite this

Alachiotis, N., & Stamatakis, A. (2010). A generic and versatile architecture for inference of evolutionary trees under maximum likelihood. In Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010 (pp. 829-835). Article 5757682 (Conference Record - Asilomar Conference on Signals, Systems and Computers; Vol. 2010). IEEE. https://doi.org/10.1109/ACSSC.2010.5757682

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title = "A generic and versatile architecture for inference of evolutionary trees under maximum likelihood",

abstract = "Likelihood-based reconstruction of phylogenetic (evolutionary) trees from molecular sequence data exhibits extreme resource requirements because of the high computational cost of the phylogenetic likelihood function. We propose a dedicated computer architecture for the inference of phylogenies under the maximum likelihood criterion. Our design is sufficiently generic to support any possible input data type, that is, DNA, RNA secondary structure, or protein data. Furthermore, the architecture is able to calculate log-likelihood scores and perform numerical scaling to maintain numerical stability on large datasets. It can also optimize the branch lengths of tree topologies and calculate transition probability matrices. We used FPGA technology to verify the correctness of our architecture.",

author = "Nikolaos Alachiotis and Alexandros Stamatakis",

year = "2010",

doi = "10.1109/ACSSC.2010.5757682",

language = "English",

isbn = "978-1-4244-9722-5",

series = "Conference Record - Asilomar Conference on Signals, Systems and Computers",

publisher = "IEEE",

pages = "829--835",

booktitle = "Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010",

address = "United States",

note = "44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010, Asilomar 2010 ; Conference date: 07-11-2010 Through 10-11-2010",

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Alachiotis, N & Stamatakis, A 2010, A generic and versatile architecture for inference of evolutionary trees under maximum likelihood. in Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010., 5757682, Conference Record - Asilomar Conference on Signals, Systems and Computers, vol. 2010, IEEE, Piscataway, NJ, pp. 829-835, 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010, Pacific Grove, California, United States, 7/11/10. https://doi.org/10.1109/ACSSC.2010.5757682

A generic and versatile architecture for inference of evolutionary trees under maximum likelihood. / Alachiotis, Nikolaos; Stamatakis, Alexandros.
Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010. Piscataway, NJ: IEEE, 2010. p. 829-835 5757682 (Conference Record - Asilomar Conference on Signals, Systems and Computers; Vol. 2010).

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

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AU - Stamatakis, Alexandros

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N2 - Likelihood-based reconstruction of phylogenetic (evolutionary) trees from molecular sequence data exhibits extreme resource requirements because of the high computational cost of the phylogenetic likelihood function. We propose a dedicated computer architecture for the inference of phylogenies under the maximum likelihood criterion. Our design is sufficiently generic to support any possible input data type, that is, DNA, RNA secondary structure, or protein data. Furthermore, the architecture is able to calculate log-likelihood scores and perform numerical scaling to maintain numerical stability on large datasets. It can also optimize the branch lengths of tree topologies and calculate transition probability matrices. We used FPGA technology to verify the correctness of our architecture.

AB - Likelihood-based reconstruction of phylogenetic (evolutionary) trees from molecular sequence data exhibits extreme resource requirements because of the high computational cost of the phylogenetic likelihood function. We propose a dedicated computer architecture for the inference of phylogenies under the maximum likelihood criterion. Our design is sufficiently generic to support any possible input data type, that is, DNA, RNA secondary structure, or protein data. Furthermore, the architecture is able to calculate log-likelihood scores and perform numerical scaling to maintain numerical stability on large datasets. It can also optimize the branch lengths of tree topologies and calculate transition probability matrices. We used FPGA technology to verify the correctness of our architecture.

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DO - 10.1109/ACSSC.2010.5757682

M3 - Conference contribution

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SN - 978-1-4244-9722-5

T3 - Conference Record - Asilomar Conference on Signals, Systems and Computers

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BT - Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010

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Alachiotis N, Stamatakis A. A generic and versatile architecture for inference of evolutionary trees under maximum likelihood. In Conference Record of the 44th Asilomar Conference on Signals, Systems and Computers, Asilomar 2010. Piscataway, NJ: IEEE. 2010. p. 829-835. 5757682. (Conference Record - Asilomar Conference on Signals, Systems and Computers). doi: 10.1109/ACSSC.2010.5757682

A generic and versatile architecture for inference of evolutionary trees under maximum likelihood

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