Phylospaces: reconstructing evolutionary trees in tuple space

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.

• Type: Conference
• Year: 2006
• Where: IPPS
• Authors: Marc L. Smith, Tiffani L. Williams
• Keywords: Cooperative Rec-I-DCM3, Distributed And Parallel Computing, Distributed Shared Memory, IPPS 2006, Tuple Space