GPU-accelerated DNA Distance Matrix Computation

Distance matrix calculation used in phylogeny analysis is computational intensive. The growing sequences data sets necessitate fast computation method. This paper accelerate Felsenstein´s DNADIST program by using OpenCL to exploit the great computation capability of graphic card. The GPU-accelerated DNADIST program achieves more than 12-fold speedup over the serial CPU program on a personal workstation with a 2.66GHz quad-core Intel CPU and an AMD HD5850 graphics card. And dual HD5850 cards on the same platform perform linear improvement of 24-fold speedup. The program also shows good performance portability by achieving 16-fold speedup with a NVIDIA Tesla C2050 card.