: A High-throughput Tool for Alignment-free Phylogenetics

Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present , a novel high-throughput tool for alignment-free phylogenetic analysis. computes the pairwise distance matrix between molecular sequences, using seven widely accepted -mer based distance measures. Based on the distance matrix, constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, was found to be the most accurate tool among all five tools compared and was 19% more accurate than , a high-accuracy multiple sequence aligner. Above all, was tens to hundreds of times faster than , which helps eliminate the computation limit currently encountered in large-scale multiple sequence alignment. is freely available at https://github.com/labxscut/ksak.