All the results are stored in the input_files folder, and each subfolder has a detailed readme file explaining its content.
For example, the folder input_files/fish/Analysis/IGC1_forceTau_Homo/Pillar211R contains the Run.py file to perform the analysis of Pillar 211 data set where all ingroup species have 2 paralogs present under the model.
Here is a list of folder name convention with their corresponding model as described in the manuscript.
| Model name in folder | Model in manuscript |
|---|---|
Original |
|
Homo |
|
forceTau |
|
forceTau_Homo |
Swap tests use reduced datasets that only contain two paralogs of DNA sequence from ingroup species, and one paralog of DNA sequence from an outgroup species. Therefore, there are only five sequences for each dataset in swap tests. Please refer to the readme file in fish and yeast folder for detailed choice os these species.
swap/unswap: when swapping the data, we swap the sequence of paralog 2 between two ingroup species.
switch/unswitch: when switching the data, we exchange the sequence between ingroup species 1 paralog 1 and ingroup species 2 paralog2.
Here are two figures showing the cases for the fish and yeast data sets:
To reproduce the results, you need to install the IGCexpansion software. The installation instruction and tutorial are at: https://github.com/xji3/IGCexpansion.git
After installing the IGCexpansion software, you can run the script Run.py in each Pillar folder to get the results.
