skills/bioskills/bio-comparative-genomics-positive-selection/scripts/selection_analysis.py

• write_codeml_control · function · L9-L66 — def write_codeml_control(alignment, tree, outfile, model='M8', output_dir='.')
• run_codeml · function · L69-L77 — def run_codeml(ctl_file, work_dir='.')
• parse_mlc_file · function · L80-L137 — def parse_mlc_file(mlc_file)
• likelihood_ratio_test · function · L140-L162 — def likelihood_ratio_test(lnL_null, lnL_alt, df)
• summarize_selection_test · function · L165-L193 — def summarize_selection_test(m7_results, m8_results)