Brief description of what the scripts do.

1. Wrapper_script.sh: The full set of commands used to run each of the scripts described below.
2. ORFvalidator.pl: This perl script will read in the multi-fasta file to verify validity of the ORF. It will detect in-frame stop codons, DNA "ambiguity" characters other than N, lack of stop codon at the end of the sequence and lack of start codon at the beginning of start codon.
3. gc_content.pl script was downloaded from https://raw.githubusercontent.com/DamienFr/GC-content-in-sliding-window-/master/perl_script.pl
4. Alignment_QC.sh: Run multiple MSA programs through guidance with 100 bootstraps, Compare alignments to get AOS and MOS, Perform model testing on each alignment, Build phylogenies with 1000 bootstraps, reroot and sort trees before counting topologies
5. getCombs.pl: This perl script will read in the number of species to sample (r), the list of n taxa. It will generate the list of all possible combinations nCr = n! / r! * (n - r)!. Used to perform test of relaxation using different combinations of species as the background set.
6. Relax_test.sh: Script to perform separate tests of relaxed selection on each of the species using all possible combinations of species as the background using each of the tree topologies supplied.
7. Collate_results.sh: Script to collate the results of separate tests of relaxed selection generated by the Relax_test.sh script. The output file is ready to be read in by the Rscripts used to generate the plots.
8. Figure_3/PlotFigure3.r: Rscript that will read in the collated results file, tree topology files and generate the TIFF files that result in different panels of Figure_3. All the data required to generate Figure_3 is also provided in the folder.
9. Figure_4/PlotFigure4.r: Rscript that will read in the number of reads supporting different nucleotide bases (A,C,G and T) at the stop codon position in the bam files of different individuals. The read counts per individual are calculated using the bam-readcount utility.Barplot in TIFF format will be generated by running the script and is provided as Figure_4. All the data required to generate Figure_4 is also provided in the folder.