START Folder "Example" has the data ready for a test run Folder "Done_Example" is what you should get after running the scripts on the example data Folder "Scripts_beetle" contains: get_orthologues.py get_filtered_flydata.py rmgaps.py rmtribolium.py run_slr_paml.py paml_analysis.py slr_analysis.py (requires plot.R in the same folder or update the path in the script) plot.R Folder "Beetles" (in the Example folder) has the beetledata: msa25.fasta msa2910.fasta msa42.fasta msa511.fasta msa561.fasta msa91.fasta msa929.fasta mainbeetle.sh </path/to/directory/Example/> runs everything, just update paths RESULTS beetles.results (SLR omega values of the beetles <= 2) flies.results (SLR omega values of the flies <=2) beetles_means.results (SLR omega means of every beetle msa, no filtering) flies_means.results (SLR omega means of every fly msa, no filtering) beetles_fltrd_means.results (SLR omega means of every beetle msa, skipping omegas that are over 2) flies_fltrd_means.results (SLR omega means of every fly msa, skipping omegas that are over 2) beetles.pdf (3 Slr graphs and 1 Paml graph of beetle results) flies.pdf (3 Slr graphs and 1 Paml graph of fly results) Other folders/files after the run is complete: Beetles (all the beetle data, info about the SLR run (.log, .stats)) Flies (fly data, trees from Ensembl, info about the Slr run (.log, .stats)) Slr_Beetles (accepted beetle .slr files) Slr_Flies (accepted fly .slr files) Paml_Beetles (accepted beetle .paml files) Paml_Flies (accepted fly .paml files) Excluded (skipped msa files, because not enough fly or beetle species etc) Beetlewithtribolium (original beetle .fasta files before removing tribolium) Flyensemblalign (flies aligned by Ensembl) Flygapless (fly MSA gaps removed)