Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Phylogenetic tools are fundamental to the studies of evolutionary relationships. 6Guangzhou Key Laboratory of Molecular Mechanism and Translation in Major Cardiovascular Disease, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.5Department of Cardiology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.4School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, China.3School of Mathematics, South China University of Technology, Guangzhou, Guangdong, China.2Guangzhou Boguan Telecommunication Technology Limited, Guangzhou, Guangdong, China.1School of Physics and Optoelectronics, South China University of Technology, Guangzhou, Guangdong, China.Xuemei Liu 1 † Ziqi Cheng 2 † Guohao Xu 3 Jiemin Xie 3 Xudong Liu 1 Bozhen Ren 3 Dongmei Ai 4 Yangxin Chen 5,6 * Li Charlie Xia 3 *
