biostudies-literatureUnknown14Liu XPhylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, Ksak was found to be the most accurate tool among all five tools compared and was 19% more accurate than ClustalW2, a high-accuracy multiple sequence aligner. Above all, Ksak was tens to hundreds of times faster than ClustalW2, which helps eliminate the computation limit curreFrontiers in microbiology1050130https://www.ebi.ac.uk/biostudies/studies/S-EPMC10098151biostudies-literatureKsak: A high-throughput tool for alignment-free phylogenetics.PMC10098151Liu XAi DXie JXia LCChen YXu GRen BCheng ZfalseKsak: A high-throughput tool for alignment-free phylogenetics.Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, Ksak was found to be the most accurate tool among all five tools compared and was 19% more accurate than ClustalW2, a high-accuracy multiple sequence aligner. Above all, Ksak was tens to hundreds of times faster than ClustalW2, which helps eliminate the computation limit curre2023-01-01T00:00:00Z20232025-04-04T09:58:37.353Z2025-02-19T03:30:25.159ZS-EPMC100981513706512210.3389/fmicb.2023.1050130