Here we provide scripts to reproduce the results in the paper "Dynamic programming algorithms for fast and accurate cell lineage tree reconstruction from CRISPR-based lineage tracing data".

The python scripts in B_scripts are "wrapper" or "caller" of those software commands we listed in the supplementary materials. The data files (e.g., input character matrices and output trees) are temporarily available on Box until they can be moved to a more permanent location; be sure to read this README file before downloading data. In particular, we needed to re-organize the KP-Tracer data files to improve accessibility; the bash scripts used for the reorganization are in this repository and the re-organized files are in bio_result.tar.gz.

The migration analysis is in star-study-bio-result.tar.gz. The CSV files as well as scripts for making all other plots and tables is under the summary directory.