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

ABSTRACT:

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 yea

SUBMITTER: Wang F 

PROVIDER: S-EPMC10990684 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature