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.