FiTree is a Python package for Bayesian inference of fitness landscapes via tree-structured branching processes.
pip install fitree
FiTree takes tumor mutation trees as input and learns a matrix representing the fitness effects of individual mutations as well as their pairwise interactions. We provide small examples on how to use FiTree:
For large-scale simulation studies and real data application, we recommend looking into the snakemake workflows.
Our paper is available as a preprint on bioRxiv. All data and code necessary to reproduce the figures and analyses presented in the paper can be found in the analysis folder.