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bioRxiv · 10.1101/2024.03.25.586513

The iPhylo Suite: An Interactive Platform for Building and Annotating Biological and Chemical Taxonomic Trees

Li, Y.·Peng, C.·Chi, F.·Huang, Z.·Yuan, M.·Jiang, C.
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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 lacking. We present the iPhylo suite (https://www.iphylo.net/), a comprehensive, automated, and interactive platform for biological and chemical taxonomic analysis. The iPhylo suite includes the Tree and Visual web-based modules for interactive building and annotating biological and chemical taxonomic trees, and a stand- alone command-line interface (CLI) module for local use and deployment on high-performance computing clusters. Furthermore, the iPhylo visualization module is fully implemented in R, allowing users to save progress locally and modify the underlying R codes. Finally, the iPhylo CLI module extends the analysis to all hierarchical relational databases. In summary, the iPhylo suite provides an integrated interactive framework for in-depth taxonomic analyses of biological and chemical features and beyond. HighlightsO_LIA platform for both biological and chemical classification analysis and visualizations. C_LIO_LIA stand-alone Command line interface module for local or HPC deployment. C_LIO_LIR-based interactive visualization module with session-saving options. C_LIO_LISupports customized hierarchical databases for analysis beyond taxonomy. C_LI

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Li, Y., Peng, C., Chi, F., Huang, Z., Yuan, M., Jiang, C.. 2024-03-28. The iPhylo Suite: An Interactive Platform for Building and Annotating Biological and Chemical Taxonomic Trees. https://doi.org/10.1101/2024.03.25.586513

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