{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["14"],"submitter":["Liu X"],"pubmed_abstract":["Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present <i>Ksak</i>, a novel high-throughput tool for alignment-free phylogenetic analysis. <i>Ksak</i> computes the pairwise distance matrix between molecular sequences, using seven widely accepted <i>k</i>-mer based distance measures. Based on the distance matrix, <i>Ksak</i> constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, <i>Ksak</i> was found to be the most accurate tool among all five tools compared and was 19% more accurate than <i>ClustalW2</i>, a high-accuracy multiple sequence aligner. Above all, <i>Ksak</i> was tens to hundreds of times faster than <i>ClustalW2</i>, which helps eliminate the computation limit curre"],"journal":["Frontiers in microbiology"],"pagination":["1050130"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10098151"],"repository":["biostudies-literature"],"pubmed_title":["<i>Ksak</i>: A high-throughput tool for alignment-free phylogenetics."],"pmcid":["PMC10098151"],"pubmed_authors":["Liu X","Ai D","Xie J","Xia LC","Chen Y","Xu G","Ren B","Cheng Z"],"additional_accession":[]},"is_claimable":false,"name":"<i>Ksak</i>: A high-throughput tool for alignment-free phylogenetics.","description":"Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present <i>Ksak</i>, a novel high-throughput tool for alignment-free phylogenetic analysis. <i>Ksak</i> computes the pairwise distance matrix between molecular sequences, using seven widely accepted <i>k</i>-mer based distance measures. Based on the distance matrix, <i>Ksak</i> constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, <i>Ksak</i> was found to be the most accurate tool among all five tools compared and was 19% more accurate than <i>ClustalW2</i>, a high-accuracy multiple sequence aligner. Above all, <i>Ksak</i> was tens to hundreds of times faster than <i>ClustalW2</i>, which helps eliminate the computation limit curre","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023","modification":"2025-04-04T09:58:37.353Z","creation":"2025-02-19T03:30:25.159Z"},"accession":"S-EPMC10098151","cross_references":{"pubmed":["37065122"],"doi":["10.3389/fmicb.2023.1050130"]}}