R Scripts and Data Files

All selection scan and differential expression results (PAML results, HyPhy results, Sleuth results), and all scripts for subsequent analyses. There are seven modules that include and R script, directory with any necessary input data, and directory with any output files. The scripts do the following: 1. process all PAML and HyPhy output into analysis-ready formats. 2. Annotate all HOGs with NCBI and Ensembl gene IDs. 3. General dataset statistic calculations 4. Bird KEGG pathway enrichment analyses. 5. Comparisons of bird and mammal selection scan results 6. Clustering and analysis of bird aBS-REL results. 7. Transcriptome analyses for both birds and mammals.