skills/bioskills/bio-comparative-genomics-ancestral-reconstruction/scripts/ancestral_reconstruction.py

• write_asr_control · function · L8-L41 — def write_asr_control(alignment, tree, outfile, output_dir='.')
• parse_rst_ancestors · function · L44-L77 — def parse_rst_ancestors(rst_file)
• extract_site_probabilities · function · L80-L113 — def extract_site_probabilities(rst_file)
• assess_reconstruction_quality · function · L116-L157 — def assess_reconstruction_quality(site_probs)
• identify_ambiguous_sites · function · L160-L166 — def identify_ambiguous_sites(site_probs, threshold=0.8)
• summarize_asr_results · function · L169-L190 — def summarize_asr_results(ancestors, quality_metrics, ambiguous_sites)