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Hierachical tree visualization of a molecule library

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ChemTreeMap screenshot


ChemTreeMap is an Open Source interactive application for visualizing chemical similarity/diversity in a molecule library.

For detailed documentation, please check ChemTreeMap on readthedocs


ChemTreeMap contains two parts: frontend (JavaScript) and backend (Python). Users can install ChemTreeMap backend as python package. We support two ways to install ChemTreeMap.

Docker installation (fastest install)

Docker is a system which can be used to build self contained versions of a Linux operating system running on your machine. When you install and run ChemTreeMap via Docker, it completely isolates the installation from pre-existing packages on your machine.

Please follow the following steps to install ChemTreeMap Docker container. (Superuser privilege may be necessary for the following commands)

See installing Docker for instructions on installing Docker on your machine.

After Docker is installed, pull ChemTreeMap image as follows.

$ docker pull ajing/chemtreemap

Then, launch a Docker container with the binary image as follows.

$ docker run -t -i -p 8000:8000 ajing/chemtreemap /bin/bash

The example code is in /examples folder. Please read and run the file to see how it works with example input files.

$ cd examples
$ python

Then, open the following URL in your Chrome/Firefox.


'aff' may be changed to your input filename without file extension.

If you have your own molecule files, please prepare your input file following the same tab delimited format as example files (e.g. aff.txt, factorxa.txt, etc.). The following command can be used to import files into Docker container.

docker cp foo.txt ajing/chemtreemap:/examples/foo.txt

Please change (variables input_file, out_file) accordingly and run the


What can you do with ChemTreeMap.

Some tips about using ChemTreeMap.

Examples to use ChemTreeMap.

Examples for the overlap between large datasets (Please use Chrome or Firefox for large datasets)

Examples for SAR analysis

Who am I?

I am @ajing, a Bioinformatics PhD student from University of Michigan. I am working under the supervision of Dr. Heather Carlson's lab. If you have any question about the project or find any bug, please check out the Wiki first, or contact ajing.



If you use our tool, please cite:

ChemTreeMap: An Interactive Map of Biochemical Similarity in Molecular Datasets. submitted to Bioinformatics