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Sys_Bio_Suppl_Feb25_2019/56_plastid_genes/_readme.txt

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+This directory contains three subdirectories with files and instructions for running 
+pair-wise Bayes Factor test for Volvocales data and create an output for Figure 2.
+
+Instructions:
+
+1. To create all possible combinations (1540 possible pairs) and submission scripts for 
+    pair wise BF test, execute gene_combos.py contained in gene_combos folder. After the 
+    MrBayes runs are completed execute capture_marglik.py to capture log-marginal likelihoods 
+    from all 1540 folder in the "output.txt".
+2. Execute deploymrbayes.py in the folder info_content to  create submission scripts 
+    and directories to compute Information content for all 56 genes using MrBayes and 
+    Galax. After the MrBayes and Galax runs are completed, executing capture_phyloinfo.py 
+    will capture the phylogenetic information contents from all 56 genes after the runs 
+    are completed.
+3. Results from 1 (output.txt) and 2 (Ipct_output.txt) are used to create the java script 
+    file cpgenedata.js which is run using d3 in the folder chunky_compat_taxa to create 
+    Figure 2.
+