Metadata-Version: 2.1
Name: fitree
Version: 0.1.0
Summary: 
Author: Computational Biology Group
Requires-Python: >=3.11,<3.13
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: anytree (>=2.9.0,<3.0.0)
Requires-Dist: graphviz (>=0.20.3,<0.21.0)
Requires-Dist: ipython (>=8.28.0,<9.0.0)
Requires-Dist: jax (>=0.4.30,<0.5.0)
Requires-Dist: numpy (>=1.26.0,<2.0.0)
Requires-Dist: pymc (>=5.8.2,<6.0.0)
Requires-Dist: scipy (>=1.14.1,<2.0.0)
Requires-Dist: seaborn (>=0.13.2,<0.14.0)
Requires-Dist: snakemake (>=8.14.0,<9.0.0)
Description-Content-Type: text/markdown

# 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](demo/AML/process_trees.ipynb)

2. [Tree generation and inference](demo/simulations/simulation.ipynb)

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


## Preprint

The preprint of the paper is provided [here](https://www.biorxiv.org/content/10.1101/2025.01.24.634649v1).


