Title:
ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony
ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony
Author(s)
Bader, David A.
Chandu, Vaddadi P.
Yan, Mi
Chandu, Vaddadi P.
Yan, Mi
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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.
Sponsor
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.
Date Issued
2006-02-26
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Technical Report