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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


  1. Clone the package as so: git clone

  2. Ensure that you have python3.6 installed. You can install this via pip.

  3. Make 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. Install Cassiopeia by first making sure you have stable version of Cython and pytest. Then, you can install Cassiopeia by running make install from the directory where you have Cassiopeia downloaded.

To verify that it installed correctly, 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