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Molecular Biology and Evolution 19:1717-1726 (2002)
© 2002 Society for Molecular Biology and Evolution

Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference

Matthew J. Brauer*,1, Mark T. Holder{dagger}, Laurie A. Dries*,2, Derrick J. Zwickl*, Paul O. Lewis{dagger} and David M. Hillis*

*Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas;
{dagger}Department of Ecology and Evolutionary Biology, University of Connecticut

We investigated the usefulness of a parallel genetic algorithm for phylogenetic inference under the maximum-likelihood (ML) optimality criterion. Parallelization was accomplished by assigning each "individual" in the genetic algorithm "population" to a separate processor so that the number of processors used was equal to the size of the evolving population (plus one additional processor for the control of operations). The genetic algorithm incorporated branch-length and topological mutation, recombination, selection on the ML score, and (in some cases) migration and recombination among subpopulations. We tested this parallel genetic algorithm with large (228 taxa) data sets of both empirically observed DNA sequence data (for angiosperms) as well as simulated DNA sequence data. For both observed and simulated data, search-time improvement was nearly linear with respect to the number of processors, so the parallelization strategy appears to be highly effective at improving computation time for large phylogenetic problems using the genetic algorithm. We also explored various ways of optimizing and tuning the parameters of the genetic algorithm. Under the conditions of our analyses, we did not find the best-known solution using the genetic algorithm approach before terminating each run. We discuss some possible limitations of the current implementation of this genetic algorithm as well as of avenues for its future improvement.


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