David A. Bader
IEEE Fellow
AAAS Fellow
Professor
College of Computing
Georgia Tech
Atlanta, GA 30332


 
 

 

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

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.

Publication History

Versions of this paper appeared as:
  1. D.A. Bader, V. Chandu, and M. Yan, ``ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony,'' Proc. The 35th International Conference on Parallel Processing (ICPP), Columbus, OH, August 2006.

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Last updated: April 12, 2006

 




Computational Biology



Parallel Computing



Combinatorics