Documentation#

scphylo-tools: a python toolkit for single-cell tumor phylogenetic analysis#

scphylo-tools is a comprehensive Python toolkit designed for single-cell tumor phylogenetic analysis. It integrates efficient implementations of state-of-the-art methods to infer evolutionary trees from single-cell genotype data.

Features#

Phylogenetic Inference: Wrappers and implementations for state-of-the-art inference methods.
API & CLI: Provides a Python API as well as command-line tools.
Visualization: Built-in visualization tools.
Datasets: Access to available datasets.
Ease of Use: A unified Python interface for complex phylogenetic workflows.

Installation#

Install the Python package from PyPI:

pip install scphylo-tools

For development and the complete native stack, use Pixi. Pixi installs Python together with Graphviz, R, rpy2, ggtree, ggtreeExtra, graph-tool, and MPI from the lockfile:

git clone https://github.com/faridrashidi/scphylo-tools
cd scphylo-tools
pixi install --locked
pixi run test

The locked Pixi environments support Linux and macOS. On Windows, use WSL for the complete native and R plotting stack.

The regular PyPI wheel and source distribution remain available for users who only need the Python package. See the installation guide for the complete development environment and plotting details.

Documentation#

Detailed documentation and tutorials are available at Read the Docs.