FiTree

FiTree is a Python package for Bayesian inference of fitness landscapes via tree-structured branching processes.

Installation

pip install fitree

Getting started

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:

1. Pre-processing of tree input

2. Tree generation and inference

For large-scale simulation studies and real data application, we recommend looking into the snakemake workflows.

Preprint

The preprint of the paper is provided here. We provide the data and script to reproduce the figures in the paper here.