WebCVTree4: Phylogenetic and Taxonomic Study Platform for Prokaryotes base on Whole Genomes.

CVTree is an alignment-free methodology for inferring species phylogeny and taxonomy. This method allows for the efficient and accurate resolution of evolutionary relationships among large numbers of species based on whole-genome sequencing data. Since 2004, we have been continuously providing CVTree web services. Recently, the server has undergone a significant upgrade, culminating in the release of the WebCVTree4 platform. This upgrade involves a comprehensive update of the built-in genomic database. The core algorithm has been optimized to enable online phylogenetic reconstruction for tens of thousands of species, thereby facilitating the construction of whole-genome-based trees of life. Furthermore, we have developed a novel algorithm for comparing phylogenetic trees with established taxonomic systems, which supports rapid tree rooting, taxonomic annotation, and topology comparison. Additionally, the interactive front-end of the web interface has been enhanced to allow users to dynamically adjust tree layouts and export high-quality phylogenetic tree figures. These advancements enable WebCVTree4 to facilitate comprehensive comparative analyses that integrate whole-genome-based phylogenetic inference with taxonomy. As research in microbial evolution and taxonomy becomes increasingly dependent upon whole-genome data, WebCVTree4 will function as an efficient web-based platform to facilitate investigations in microbial phylogenetics and taxonomy. It is accessible at https://cvtree.online/.