Abstract:

PAML, which is widely used, is a package of programs for maximum likelihood phylogenetic analysis of protein and DNA sequences. However, its calculation is time consuming because of too many parameters and complex models. The paper focus on the most important part in PAML: codeml. After analyzing the algorithm and finding program bottleneck by profiling, we parallelize the bottlenecks based on the capacity of modern multicore CPU and SIMD technology in order to reduce the overall operating time. The experimental results on both real and simulated data show that our parallel algorithm for PAML can improve the calculation efficiency. The final speedup is up to 7.94.

Key words: parallel algorithm;PAML;multicore CPU;SIMD