contents: evolutionary analyses result files for PAML NS sites package and HyPhy packages FUBAR, GARD, and MEME (both using a user defined tree and using GARD generated trees).
notes: 

directory name: GARD_recombination_trees
contents: newick format trees generated by HyPhy GARD analyses for CEACAM sequences identified as containing potential recombination break points by GARD

directory name: site_selection_results
contents: directories containing result files for PAML, FUBAR, MEME with user tree, and MEME with GARD trees.
contents:

    - *_all_evo_data directories 
        o all evolutionary analysis results files data 
        o used with the code listed below to generate images for Figure 2A, Figure 2 – figure supplement 1, and Figure 4D
            - Figure 2A - source code.r (Figure 2 - source code)
            - Figure 2 - figure supplement 1- source code.r (Figure 2 - figure supplement 1- source code)
            - Figure 4D - source code.r (Figure 4 - source code)
        
        Notes: 
            - to use a *_all_evo_data directory with the code listed above directory name must be modified to "all_evo_data"
            - CCM*__NS_extracted_sites.txt files are summary files created by extracting site specific data for PAML results files (mlc files). *See below for more information 

    - original_PAML_NS_sites_files directory contains the unmodified results file (i.e. the mlc files) for PAML NS sites analyses. 
        Notes: 
        o also contains file PAML_NS_files.txt for use with scripts to extract and summarize site specific data
        o Site specific data for Naive Empirical Bayes (NEB) and Bayes Empirical Bayes (BEB) analyses run under different models of selection were extracted using 
            - PAML_NS_sites_extraction.ipynb and 
            - PAML_NS_sites_extraction.py 
            (both scripts can be found in Figure 2 - source code) 
        to generate the CCM*__NS_extracted_sites.txt summary files found in *_all_evo_data directories.
