This website serves as documentation to the Cassiopeia software suite, maintained by the Yosef Lab at UC Berkeley.

Cassiopeia [Jones20] is a package for end-to-end phylogenetic reconstruction of single-cell lineage tracing data. The package is composed of four independent modules:

  • preprocess for processing sequencing FASTQ data to character matrices

  • solver for performing tree inference

  • simulator for simulating trees and character-level data

  • plotting for plotting trees.

If you find this useful for your research, please consider citing Cassiopeia [Jones20].

installation with cassiopeia action icon

New to Cassiopeia? Check out the installation guide.

cassiopeia user guide action icon
User guide

The tutorials provide in-depth information on running Cassiopeia.

api of scvi action icon
API reference

The API reference contains a detailed description of the Cassiopeia API.

questions about cassiopeia
Questions & Issues

Have a question or found a bug? File an issue.