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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\u2019s 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.<\/jats:p>","DOI":"10.1093\/bib\/bbae679","type":"journal-article","created":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T01:29:25Z","timestamp":1735608565000},"source":"Crossref","is-referenced-by-count":4,"title":["The iPhylo suite: an interactive platform for building and annotating biological and chemical taxonomic trees"],"prefix":"10.1093","volume":"26","author":[{"given":"Yueer","family":"Li","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang 310030 ,","place":["China"]}]},{"given":"Chen","family":"Peng","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang 310030 ,","place":["China"]}]},{"given":"Fei","family":"Chi","sequence":"additional","affiliation":[{"name":"Innovation Center of Yangtze River Delta, Zhejiang University , 828 Zhongxing Road, Jiashan County, Jiaxing, Zhejiang 314103 ,","place":["China"]}]},{"given":"Zinuo","family":"Huang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang 310030 ,","place":["China"]}]},{"given":"Mengyi","family":"Yuan","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang 310030 ,","place":["China"]}]},{"given":"Xin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, 291 Campus Drive, Santa Clara County, CA 94305 ,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0260-7271","authenticated-orcid":false,"given":"Chao","family":"Jiang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang 310030 ,","place":["China"]},{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou, 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