The free tree generator and annotator

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Tree Generation

We offer rapid and concise tree generation, providing biological and chemical taxonomy trees for tens of thousands of organisms and chemicals.

Visualization & Annotation

The iPhylo Visual interactively facilitate the display, annotation, and inspection of tree-based structures, including but not limited to phylogenetic and chemical taxonomic trees.

Further Exploration

iPhylo command line interface enables customized tree creation and access to an expanded database, which is designed for local use and high-performance computing applications.


Biological & Chemical

The iPhylo database includes 2,388,300 taxids from NCBI Taxonomy and 801,308 functional compounds from MONA, GNPS, and NIST chemical compound databases.

Lipids and lipid like molecules


Organoheterocyclic compounds

Organic oxygen compounds

Organic acids and derivatives

Organic nitrogen compounds

Phenylpropanoids and polyketides


iPhylo Tree Example

Tree Of Glacier Microbiome

A phylogenetic tree of 968 species-level glacier microbiomes from Tibetan glacier. We construct a customized tree that incorporated the GTDB classification using iPhylo Visual.

Chemical Classification Tree

A representative chemical taxonomy tree made by iPhylo based on chemical InChIKeys, representing superclass, class, and subclass with different color partitions on the outer ring.

Tree Of Gut Microbiome

A phylogenetic tree constructed using NCBI taxonomy IDs, with branches color-coded by phyla. It profiles the metabolite biosynthetic abundance for individual bacterial strains in the gut microbiome.

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