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Paper Abstract and Keywords
Presentation 2013-05-20 15:00
An FPGA Implementation of the Progressive Tree Neighborhood Algorithm -- Phylogenetic Tree Reconstruction with Maximum Parsimony --
Henry Block, Tsutomu Maruyama (Univ. of Tsukuba) RECONF2013-2
Abstract (in Japanese) (See Japanese page) 
(in English) In this paper, we present an FPGA-hardware implementation for the progressive tree neighborhood algorithm applied to phylogenetic tree reconstruction with maximum parsimony. The proposed hardware architecture is modular, and has pipelined stages to improve the performance and reduce the execution time of the algorithm. Implementation results for a specific problem showed a 1247x acceleration compared to a C++ software implementation.
Keyword (in Japanese) (See Japanese page) 
(in English) FPGA / Bioinformatics / Acceleration / Parsimony / / / /  
Reference Info. IEICE Tech. Rep., vol. 113, no. 52, RECONF2013-2, pp. 7-12, May 2013.
Paper # RECONF2013-2 
Date of Issue 2013-05-13 (RECONF) 
ISSN Print edition: ISSN 0913-5685  Online edition: ISSN 2432-6380
All rights are reserved and no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Notwithstanding, instructors are permitted to photocopy isolated articles for noncommercial classroom use without fee. (License No.: 10GA0019/12GB0052/13GB0056/17GB0034/18GB0034)
Download PDF RECONF2013-2

Conference Information
Committee RECONF  
Conference Date 2013-05-20 - 2013-05-21 
Place (in Japanese) (See Japanese page) 
Place (in English) Kochi Prefectural Culture Hall 
Topics (in Japanese) (See Japanese page) 
Topics (in English) Reconfigurable Systems, etc. 
Paper Information
Registration To RECONF 
Conference Code 2013-05-RECONF 
Language English 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) An FPGA Implementation of the Progressive Tree Neighborhood Algorithm 
Sub Title (in English) Phylogenetic Tree Reconstruction with Maximum Parsimony 
Keyword(1) FPGA  
Keyword(2) Bioinformatics  
Keyword(3) Acceleration  
Keyword(4) Parsimony  
1st Author's Name Henry Block  
1st Author's Affiliation University of Tsukuba (Univ. of Tsukuba)
2nd Author's Name Tsutomu Maruyama  
2nd Author's Affiliation University of Tsukuba (Univ. of Tsukuba)
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Speaker Author-1 
Date Time 2013-05-20 15:00:00 
Presentation Time 25 minutes 
Registration for RECONF 
Paper # RECONF2013-2 
Volume (vol) vol.113 
Number (no) no.52 
Page pp.7-12 
Date of Issue 2013-05-13 (RECONF) 

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