WebCVTree4: A Newly Designed Phylogenetic and Taxonomic Study Platform for Prokaryotes Using Composition Vectors and Whole Genomes

TL;DR

WebCVTree4 is an upgraded online platform for large-scale phylogenetic and taxonomic analysis of prokaryotes using alignment-free methods, supporting dynamic visualization and comparison with existing taxonomies.

Contribution

The platform introduces a comprehensive database update, optimized core algorithms for large datasets, and novel tree comparison algorithms with interactive visualization tools.

Findings

Supports online reconstruction of trees for tens of thousands of species

Enables rapid comparison of phylogenetic trees with taxonomic systems

Provides high-quality exportable phylogenetic tree figures

Abstract

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 sequence 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 encompasses a comprehensive update of the inbuilt genomic database. Concurrently, the core algorithm has been optimized to support online phylogenetic reconstruction for tens of thousands of species, thereby facilitating the construction of genome-based trees of life. Moreover, we have developed a novel algorithm for comparing phylogenetic trees with established taxonomic systems. This algorithm allows for rapid tree rooting, taxonomic annotation, and topology comparison. Through an interactive web-based visualization tool, users can dynamically adjust tree layouts and export high-quality phylogenetic tree figures. This functionality provides robust support for comparative analysis between CVTree-generated phylogeny and taxonomy. As genome sequencing costs continue to decline, research into microbial evolution and the revision of taxonomic frameworks will increasingly rely on whole-genome data. WebCVTree4 will serve as an efficient web-based platform to support studies in microbial phylogenetics and taxonomy, accessible at https://cvtree.online/.