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 |
Copyright and reproduction |
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 |
Keyword(5) |
|
Keyword(6) |
|
Keyword(7) |
|
Keyword(8) |
|
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) |
3rd Author's Name |
|
3rd Author's Affiliation |
() |
4th Author's Name |
|
4th Author's Affiliation |
() |
5th Author's Name |
|
5th Author's Affiliation |
() |
6th Author's Name |
|
6th Author's Affiliation |
() |
7th Author's Name |
|
7th Author's Affiliation |
() |
8th Author's Name |
|
8th Author's Affiliation |
() |
9th Author's Name |
|
9th Author's Affiliation |
() |
10th Author's Name |
|
10th Author's Affiliation |
() |
11th Author's Name |
|
11th Author's Affiliation |
() |
12th Author's Name |
|
12th Author's Affiliation |
() |
13th Author's Name |
|
13th Author's Affiliation |
() |
14th Author's Name |
|
14th Author's Affiliation |
() |
15th Author's Name |
|
15th Author's Affiliation |
() |
16th Author's Name |
|
16th Author's Affiliation |
() |
17th Author's Name |
|
17th Author's Affiliation |
() |
18th Author's Name |
|
18th Author's Affiliation |
() |
19th Author's Name |
|
19th Author's Affiliation |
() |
20th Author's Name |
|
20th Author's Affiliation |
() |
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 |
#Pages |
6 |
Date of Issue |
2013-05-13 (RECONF) |
|