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

Wang, Fang1,2; Wang, Yibin2; Zeng, Xiaofei3; Zhang, Shengcheng2; Yu, Jiaxin2; Li, Dongxi1; Zhang, Xingtan2

2024-03-29

10.1093/bioinformatics/btae154

BIOINFORMATICS   影响因子和分区

1367-4803

1367-4811

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.Availability and implementation MIKE is publicly available on Github at https://github.com/Argonum-Clever2/mike.git.

SCI

英语

其他

Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics

Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability

WOS:001196753100004

OXFORD UNIV PRESS

BIOLOGY & BIOCHEMISTRY

Web of Science

1.Taiyuan Univ Technol, Coll Comp Sci & Technol, Taiyuan 030024, Shanxi, Peoples R China
2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Natl Key Lab Trop Crop Breeding, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,G, Shenzhen 518120, Guangdong, Peoples R China
3.Southern Univ Sci & Technol, Joint Lab Guangdong Hong Kong Univ Vasc Homeostasi, Sch Med, Dept Human Cell Biol & Genet, Shenzhen 508055, Guangdong, Peoples R China

Wang, Fang,Wang, Yibin,Zeng, Xiaofei,et al. MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction[J]. BIOINFORMATICS,2024,40(4).

Wang, Fang.,Wang, Yibin.,Zeng, Xiaofei.,Zhang, Shengcheng.,Yu, Jiaxin.,...&Zhang, Xingtan.(2024).MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.BIOINFORMATICS,40(4).

Wang, Fang,et al."MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction".BIOINFORMATICS 40.4(2024).