4.6 Article

Ksak: A high-throughput tool for alignment-free phylogenetics

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FRONTIERS IN MICROBIOLOGY
卷 14, 期 -, 页码 -

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FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2023.1050130

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k-mer; phylogentic tree; alignment free; open source; microbiome

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In this paper, a novel high-throughput tool called Ksak is introduced for alignment-free phylogenetic analysis. Ksak computes pairwise distance matrix using seven widely accepted k-mer based distance measures and constructs the phylogenetic tree with standard algorithms. Benchmarking results show that Ksak is the most accurate tool among five compared tools, outperforming ClustalW2, a high-accuracy multiple sequence aligner, by 19%. Moreover, Ksak is tens to hundreds of times faster than ClustalW2, addressing the computation limit in large-scale multiple sequence alignment. Ksak is freely available.
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 currently encountered in large-scale multiple sequence alignment. Ksak is freely available at .

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