Generative communication in Linda
ACM Transactions on Programming Languages and Systems (TOPLAS)
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction
International Journal of Bioinformatics Research and Applications
Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood
HPCC'05 Proceedings of the First international conference on High Performance Computing and Communications
Parallelism and evolutionary algorithms
IEEE Transactions on Evolutionary Computation
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Phylospaces is a novel framework for reconstructing evolutionary trees in tuple space, a distributed shared memory that permits processes to communicate and coordinate with each other. Our choice of tuple space as a concurrency model is somewhat unusual, given the prominence and success of pure message passing models, such as MPI. We use Phylospaces to devise Cooperative Rec-I-DCM3, a population-based strategy for navigating tree space. Cooperative Rec-I-DCM3 is based on Rec-I-DCM3, the fastest sequential algorithm under maximum parsimony. We compare the performance of the algorithms on two datasets consisting of 2,000 and 7,769 taxa, respectively. Our results demonstrate that Cooperative Rec-I-DCM3 outperforms its sequential counterpart by at least an order of magnitude.