Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
Finding an Optimal Inversion Median: Experimental Results
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
IEA/AIE '02 Proceedings of the 15th international conference on Industrial and engineering applications of artificial intelligence and expert systems: developments in applied artificial intelligence
A Hardware Genetic Algorithm for the Travelling Salesman Problem on SPLASH 2
FPL '95 Proceedings of the 5th International Workshop on Field-Programmable Logic and Applications
Genetic Algorithms Using Parallelism and FPGAs: The TSP as Case Study
ICPPW '05 Proceedings of the 2005 International Conference on Parallel Processing Workshops
Is high-performance reconfigurable computing the next supercomputing paradigm?
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Motion Compensation and Reconstruction of H.264/AVC Video Bitstreams using the GPU
WIAMIS '07 Proceedings of the Eight International Workshop on Image Analysis for Multimedia Interactive Services
A General Reconfigurable Architecture for the BLAST Algorithm
Journal of VLSI Signal Processing Systems
Parallel processing between GPU and CPU: Concepts in a game architecture
CGIV '07 Proceedings of the Computer Graphics, Imaging and Visualisation
FPGA Acceleration of Gene Rearrangement Analysis
FCCM '07 Proceedings of the 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
FCCM '07 Proceedings of the 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
High performance phylogenetic analysis with maximum parsimony on reconfigurable hardware
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
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In this paper, we describe the design for a co-processor for whole-genome phylogenetic reconstruction. Our current design performs a parallelized breakpoint median computation, which is an expensive component of the overall application. When implemented on a field-programmable gate array (FPGA), our hardware breakpoint median achieves a maximum speedup of 1005× over software. When the coprocessor is used to accelerate the entire reconstruction procedure, we achieve a maximum application speedup of 417×. The results in this paper suggest that FPGA-based acceleration is a promising approach for computationally expensive phylogenetic problems, in spite of the fact that the involved algorithms are based on complex, control-dependent combinatorial optimization.