← Về thư mục
skills/bioskills/bio-epidemiological-genomics-phylodynamics/scripts/treetime_analysis.py
- to_decimal_year · function · L24-L34 — def to_decimal_year(date_str)
- prepare_dates_tsv · function · L37-L42 — def prepare_dates_tsv(metadata_df, name_col, date_col, out_path)
- root_to_tip_regression · function · L45-L75 — def root_to_tip_regression(treetime_outdir)
- assert_temporal_signal · function · L78-L81 — def assert_temporal_signal(r2)
- run_iqtree · function · L84-L88 — def run_iqtree(aln_path, prefix, model='GTR+G', ascertainment_bias=False, threads='AUTO')
- run_treetime · function · L91-L98 — def run_treetime(tree_path, aln_path, dates_path, out_dir, clock_filter=TREETIME_CLOCK_FILTER)
- run_date_randomisation · function · L101-L107 — def run_date_randomisation(tree_path, dates_path, out_dir)
- run_gubbins · function · L110-L119 — def run_gubbins(core_full_aln_path, prefix='gubbins')
- validate_bdsky_origin · function · L122-L126 — def validate_bdsky_origin(origin, root_height)
- suggest_bdsky_origin · function · L129-L130 — def suggest_bdsky_origin(root_height)
- run_beast2 · function · L133-L140 — def run_beast2(xml_path, seed=42, threads=4, log_prefix=None)
- combine_chains · function · L143-L153 — def combine_chains(log_files, trees_files, out_log, out_trees, burnin_pct=BEAST_BURNIN_PCT)
- loganalyser_ess · function · L156-L159 — def loganalyser_ess(log_file, burnin_pct=BEAST_BURNIN_PCT)
- validate_mascot_deme_sizes · function · L162-L166 — def validate_mascot_deme_sizes(deme_counts)
- bacterial_phylodynamics_pipeline · function · L169-L189 — def bacterial_phylodynamics_pipeline(core_full_aln, dates_tsv, work_dir, species_reference_clock=S_PNEUMO_REFERENCE_CLOCK)