Scripts

Scripts used to calculate average pairwise differences between all 6 pairwise combinations along the XR chromosome between Drosophila pseudoobscura, Drosophila persimilis, Sex-Ratio Drosophila persimilis, and Drosophila miranda. These output file can then be used to calculate RND between
D pseudoobscura, D persimilis, and SR D persimilis in another program such as Microsoft Excel. All scripts are written in Perl. Author: Kenneth Hoehn. Date: May-5-2011. Sections: 1. Constructing the combined, raw input file from PILEUP outputs (skip if combined input file is provided); 2. Necessary input files for final analysis; 3. Editing combined input file and calculating average pairwise differences; 4. Calculating RND; 5. Double checking output; 6. Simple window writing script. See README.txt for more details.