SCRIPTS LIST

name: Figure 2A - source code.r
use: to generate images for Figure 2A
notes:
    - directions for running the program in R found within the file under SETUP
    - use with Figure 2 - source data 3
    - same data files as for Figure 2 - figure supplement 1 - source code and Figure 4 - source code

name: PAML_NS_sites_extraction.ipynb
name: PAML_NS_sites_extraction.py
use: together these scripts create the CCM*__NS_extracted_sites.txt files used to create graphs for Figure 2A, Figure 2 - figure supplement 1 and Figure 4A
notes: 
    - the jupyter code (PAML_NS_sites_extraction.ipynb) runs the python script (PAML_NS_sites_extraction.py)
    - to run code open PAML_NS_sites_extraction.ipynb in jupyter
    - all other instructions for running the code contained within PAML_NS_sites_extraction.ipynb when opened in jupyter 