Enhancement of Computational Efficiency of Alignment-Free Multiple Sequence Comparison through Parallelization

Alignment-free multiple sequence comparison based on the concept of comparing the similarity/ dissimilarity between two Markov models is significantly improvised using parallel control flow structure. The present study implements a MATLAB-based down-link physical-layer simulator for construction of pair-wise distance matrix by comparing two Markov Models using Kullback–Leibler divergence. The pair-wise distance matrix is used for constructing guide tree for finding the multiple sequence alignment. By utilizing the Parallel Computing Toolbox of MATLAB, the parallel control flow structure significantly reduced the simulation time on multi-core processors.