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Cassiopeia: A pipeline for single-cell lineage tracing data

Cassiopeia is an end-to-end pipeline for single-cell lineage tracing experiments. The software contained here comes equipped with modules for processing sequencing reads, reconstructing & plotting trees, analyzing these trees, and benchmarking new algorithms.

You can find all of our documentation here.

We also have provided tutorials for three modules:

You can also find our originally describing Cassiopeia published in Genome Biology.

Free Software: MIT License


For users:

pip install git+

For developers:

  1. Clone the package as so: git clone

  2. Ensure that you have Python >= 3.8 installed. (Due to dependencies no longer supporting Python 3.7, we have now stopped supporting Python <= 3.7) We prefer using miniconda.

  3. [Optional] If you intend to use the CassiopeiaILP solver, please be sure that Gurobi is installed. You can follow the instructions listed here. To verify that it's working correctly, use the following tests:

    • Run the command from a terminal window
    • From the Gurobi installation directory (where there is a file), use python install --user
  4. [Optional] To use fast versions of Neighbor-Joining and UPGMA, install CCPhylo then set ccphylo_path in the config.ini file in the cassiopeia directory.

  5. Install Cassiopeia by first changing into the Cassiopeia directory and then pip3 install .. To install dev and docs requirements, you can run pip3 install .[dev,docs].

  6. [Optional] To use tools built for the analysis of spatial lineage tracing datasets, you can install Cassiopeia with pip install .[spatial]. Please note that we recommend using Python >= 3.9 for these analyses as some features might not be available otherwise, due to package dependencies (especially 3D visualization).

To verify that it installed correctly, install pytest (pip install pytest) and try running our tests with make test.


If you've found Cassiopeia useful for your research, please consider citing our paper published in Genome Biology:

Matthew G Jones*, Alex Khodaverdian*, Jeffrey J Quinn*, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonathan S Weissman, Nir Yosef. (2020), Inference of single-cell phylogenies from lineage tracing data using Cassiopeia, Genome Biology