This repository is for evaluating and developing methods for inferring phylogenetic trees from CRISPR lineage tracing data. Cassiopeia and Wilson's phylogeny repository must be installed in the same directory as this repository. For the latter, note that PAUP, PhyML, and BioNJ do not need to be installed for the code here to work.

So far, several methods have been evaluated, and the next step is to modify the method described in Wilson 2021 to give it a mutation model more appropriate for CRISPR lineage tracing.