数字农科院2.0

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction

文献类型： 外文期刊

作者： Fang Wang;Yibin Wang;Xiaofei Zeng;Shengcheng Zhang;Jiaxin Yu;Dongxi Li;Xingtan Zhang

作者机构：

关键词： （1-1-2）

期刊名称： Bioinformatics

ISSN： 1367-4803

年卷期： 2024 年 40 卷 4 期

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收录情况： SCIE（2024版）

摘要： Motivation: Constructing a phylogenetic tree requires calculating the evolutionary distance between samples or species via large-scale resequencing data, a process that is both time-consuming and computationally demanding. Striking the right balance between accuracy and efficiency is a significant challenge. Results: To address this, we introduce a new algorithm, MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

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