IGCexpansion

IGC expansion development folder

Dependent software:

jsonctmctree package (powerful likelihood calculation engine by Alex Griffing)

Biopython networkx numpy scipy

(you could install them by

pip install --user Biopython networkx numpy scipy)

Coding Language

Python 3.6 or higher

Preparation

Mac OS / Linux

To install python packages, you need to use pip (package management).
You might need to install git.

Windows

I recommand using Anaconda on Windows that ships with pip functionality and many more useful features.
You still need to install git

Install python packages

Install jsonctmctree package by Alex Griffing (slightly modified for version updates):

pip install --user git+https://github.com/xji3/jsonctmctree.git

Install IGCexpansion package:

pip install --user git+https://github.com/xji3/IGCexpansion.git

Similarly install any other python packages (they should have been installed with IGCexpansion already)

pip install --user networkx

pip install --user Biopython

To uninstall:

pip uninstall IGCexpansion

Getting a local copy of the package

git clone https://github.com/xji3/IGCexpansion.git

You can now run the tutorial file or edit it to perform analyses.

cd IGCexpansion/tutorials/IS_IGC

python Run_IS_IGC.py

Tutorials

For independent site IGC (IS-IGC) analyses, please refer to this tutorial.
There are two versions of the software that implement the same IS-IGC approach. The difference between them is the flexibility of considering different duplication/loss histories where the first version assumes one single duplication event without loss which the second version does not.