Title:
ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony

dc.contributor.author Bader, David A.
dc.contributor.author Chandu, Vaddadi P.
dc.contributor.author Yan, Mi
dc.date.accessioned 2007-05-21T21:18:43Z
dc.date.available 2007-05-21T21:18:43Z
dc.date.issued 2006-02-26
dc.description.abstract Constructing phylogenetic trees in the study of the evolutionary history of a group organisms is an extremely challenging problem in computational biology. The problem becomes intractable with growing number of organisms. In this paper, we design and implement an efficient parallel solver (ExactMP) using a parsimony based approach for solving this problem. We create a testbed consisting of eighteen datasets of varying size (up to 27 taxa) and difficulty level (easy to hard), containing real (Eukaryotes, Metazoan, and rbcL) and randomly-generated synthetic genome sequences. We demonstrate our ExactMP Solver against this testbed and achieve a parallel speedup of up to 7.26 with 8 processors using an 8-way symmetric multiprocessor. The main contributions of this work are: (1) an efficient parallel solver ExactMP for the problem of phylogenetic tree reconstruction using maximum parsimony, (2) a new upper bounding methodology for this problem using heuristic and randomization techniques, and (3) a highly optimized branch and bound algorithm for this problem. en
dc.description.sponsorship This work was supported in part by NSF Grants CAREER CCF-0611589, ACI-00-93039, NSF DBI- 0420513, ITR ACI-00-81404, DEB-99-10123, ITR EIA-01-21377, Biocomplexity DEB-01-20709, and ITR EF/BIO 03-31654; and DARPA Contract NBCH30390004. en
dc.identifier.uri http://hdl.handle.net/1853/14425
dc.language.iso en_US en
dc.publisher Georgia Institute of Technology en
dc.relation.ispartofseries CSE Technical Reports; GT-CSE-06-11 en
dc.subject Computational biology en
dc.subject ExactMP solver en
dc.subject Heuristic algorithms en
dc.subject Parallel solver en
dc.subject Parsimony en
dc.subject Phylogenetic trees en
dc.subject Symmetric multiprocessors (SMPs) en
dc.title ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony en
dc.type Text
dc.type.genre Technical Report
dspace.entity.type Publication
local.contributor.corporatename College of Computing
local.contributor.corporatename School of Computational Science and Engineering
local.relation.ispartofseries College of Computing Technical Report Series
local.relation.ispartofseries School of Computational Science and Engineering Technical Report Series
relation.isOrgUnitOfPublication c8892b3c-8db6-4b7b-a33a-1b67f7db2021
relation.isOrgUnitOfPublication 01ab2ef1-c6da-49c9-be98-fbd1d840d2b1
relation.isSeriesOfPublication 35c9e8fc-dd67-4201-b1d5-016381ef65b8
relation.isSeriesOfPublication 5a01f926-96af-453d-a75b-abc3e0f0abb3
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
GT-CSE-06-11.pdf
Size:
387.41 KB
Format:
Adobe Portable Document Format
Description:
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.86 KB
Format:
Item-specific license agreed upon to submission
Description: