Installation

Anaconda install

The preferred way to install gctree is with Conda:

conda create -n gctree python=3.10
conda activate gctree
conda install -c conda-forge gctree

You will likely also want to install PHYLIP (see below)

Pip install

You may install using pip instead:

pip install gctree

However, you will then need to separately install PHYLIP

Docker build

You may also find the provided Dockerfile useful. The resulting image runs the test script tests/test.sh by default. This runs the default inference pipeline on the sample data provided with gctree.

git clone git@github.com:matsengrp/gctree.git
docker build gctree -t gctree

To run the test script and verify the image was built successfully:

docker run -t gctree

Or use the image interactively with, for example:

docker run -i -t gctree bash

PHYLIP Installation

The original use case for gctree is to use genotype abundance information to rank degenerate maximum parsimony trees. For this, you will need Joe Felsenstein’s PHYLIP package (https://evolution.genetics.washington.edu/phylip.html). If you are working in a Conda environment, PHYLIP can be installed with

conda install -c bioconda phylip