Abstract
Accurate and rapid taxonomic classifications are essential for systematically exploring organisms and metabolites in diverse environments. Many tools have been developed for biological taxonomic trees, but limitations apply, and a streamlined method for constructing chemical taxonomic trees is notably absent. We present the iPhylo suite (https://www.iphylo.net/), a comprehensive, automated, and interactive platform for biological and chemical taxonomic analysis. The iPhylo suite features web-based modules for the interactive construction and annotation of taxonomic trees and a stand-alone command-line interface (CLI) for local operation or deployment on high-performance computing (HPC) clusters. iPhylo supports National Center for Biotechnology Information (NCBI) taxonomy for biologicals and ChemOnt and NPClassifier for chemical classifications. The iPhylo visualization module, fully implemented in R, allows users to save progress locally and customize the underlying R code. Finally, the CLI module facilitates analysis across all hierarchical relational databases. We showcase the iPhylo suite's capabilities for visualizing environmental microbiomes, analyzing gut microbial metabolite synthesis preferences, and discovering novel correlations between microbiome and metabolome in humans and environment. Overall, the iPhylo suite is distinguished by its unified and interactive framework for in-depth taxonomic and integrative analyses of biological and chemical features and beyond.