├── .gitignore ├── LICENSE ├── README.md ├── bin ├── clustervars ├── pairtree ├── plottree ├── plotvars ├── removegarbage └── summposterior ├── comparison ├── calder │ ├── convert_inputs.py │ ├── convert_outputs.py │ └── run.sh ├── citup │ ├── convert_inputs.py │ ├── convert_outputs.py │ └── run.sh ├── convert_json_to_pickle.py ├── count_trees.py ├── enum_true_trees.py ├── eval_mutdists.py ├── eval_mutphis.py ├── eval_mutrels.py ├── eval_runtime.py ├── eval_trerror.py ├── evalutil.py ├── extract_runtimes.py ├── impute_missing_mutphis.py ├── lichee │ ├── convert_inputs.py │ ├── convert_outputs.py │ ├── replace_llh.py │ └── run.sh ├── make_baseline_mutdist_from_pairtree_run.py ├── make_baseline_mutdist_from_sims.py ├── make_mle_mutphis.py ├── make_truth_mutphi.py ├── mutdist.py ├── mutphi.py ├── mutstat.py ├── neutree │ ├── __init__.py │ ├── convert.sh │ ├── make_mutdists.py │ ├── make_mutphis.py │ ├── make_mutrel_from_best_soln.py │ └── make_mutrels.py ├── pairtree │ ├── calc_cluster_llh.py │ ├── compare_clusterings.py │ ├── compute_entropy.py │ ├── compute_entropy.sh │ ├── convert_outputs.py │ ├── convert_phylosteph_inputs.sh │ ├── convert_phylosteph_inputs_to_pairtree.py │ ├── convert_simdata_to_results.py │ ├── copy_mutrels.py │ ├── eval_garbage.py │ ├── eval_garbage.sh │ ├── eval_missedcna.sh │ ├── fix_omegas.py │ ├── insert_structure.py │ ├── make_mutrel_from_clustrel.py │ ├── make_treecmp.sh │ ├── plot_clustering.py │ ├── plot_dirichlet.py │ ├── plot_entropy.py │ ├── plot_eta_stats.py │ ├── plot_garbage.py │ ├── plot_phi_variance.py │ ├── print_llh.py │ ├── run.sh │ ├── run_clustering.sh │ ├── subset_samples.py │ ├── util.sh │ └── write_only_structs.py ├── pastri │ ├── convert_inputs.py │ ├── convert_outputs.py │ ├── pastri_util.py │ └── run.sh ├── plot_comparison.py ├── plot_comparison.sh ├── plotly │ ├── README.md │ ├── cross_trace_calc.js.diff │ └── plotly.min.js ├── plotter │ ├── __init__.py │ ├── plot_all_methods.py │ ├── plot_entropy.py │ ├── plot_sims.py │ ├── plot_single_method.py │ ├── plot_single_vs_others.py │ └── plot_steph.py ├── pwgs │ ├── convert_inputs.py │ ├── convert_outputs.py │ ├── count_clusters.py │ ├── count_clusters.sh │ ├── empty.cnv │ └── run.sh ├── run_eval.sims.sh ├── run_eval.steph.sh ├── sciclone │ ├── convert_inputs.py │ ├── convert_outputs.py │ ├── run.sh │ └── run_sciclone.R └── set_subtract_scores.py ├── convert_to_ssm ├── columns.py ├── ssm_base_converter.py └── vcf_example │ ├── example.vcf │ └── vcf_to_ssm.py ├── doc ├── TODO.txt ├── notes.txt └── versions.txt.old ├── example ├── example.params.json ├── example.ssm └── example.truth.pickle ├── inputs ├── steph.vanilla │ ├── SJBALL022609.params.json │ ├── SJBALL022609.ssm │ ├── SJBALL022610.params.json │ ├── SJBALL022610.ssm │ ├── SJBALL022610steph.params.json │ ├── SJBALL022610steph.ssm │ ├── SJBALL022611.params.json │ ├── SJBALL022611.ssm │ ├── SJBALL022612.params.json │ ├── SJBALL022612.ssm │ ├── SJBALL022613.params.json │ ├── SJBALL022613.ssm │ ├── SJBALL022614.params.json │ ├── SJBALL022614.ssm │ ├── SJBALL031.params.json │ ├── SJBALL031.ssm │ ├── SJBALL036.params.json │ ├── SJBALL036.ssm │ ├── SJERG009.params.json │ ├── SJERG009.ssm │ ├── SJETV010.params.json │ ├── SJETV010.ssm │ ├── SJETV010nohypermut.params.json │ ├── SJETV010nohypermut.ssm │ ├── SJETV010stephR1.params.json │ ├── SJETV010stephR1.ssm │ ├── SJETV010stephR1R2.params.json │ ├── SJETV010stephR1R2.ssm │ ├── SJETV010stephR2.params.json │ ├── SJETV010stephR2.ssm │ ├── SJETV043.params.json │ ├── SJETV043.ssm │ ├── SJETV047.params.json │ ├── SJETV047.ssm │ ├── SJMLL026.params.json │ ├── SJMLL026.ssm │ ├── SJMLL039.params.json │ └── SJMLL039.ssm ├── steph.xenos.nocns │ ├── SJBALL022609.params.json │ ├── SJBALL022609.ssm │ ├── SJBALL022610.params.json │ ├── SJBALL022610.ssm │ ├── SJBALL022610steph.params.json │ ├── SJBALL022610steph.ssm │ ├── SJBALL022611.params.json │ ├── SJBALL022611.ssm │ ├── SJBALL022612.params.json │ ├── SJBALL022612.ssm │ ├── SJBALL022613.params.json │ ├── SJBALL022613.ssm │ ├── SJBALL022614.params.json │ ├── SJBALL022614.ssm │ ├── SJBALL031.params.json │ ├── SJBALL031.ssm │ ├── SJBALL036.params.json │ ├── SJBALL036.ssm │ ├── SJERG009.params.json │ ├── SJERG009.ssm │ ├── SJETV010.params.json │ ├── SJETV010.ssm │ ├── SJETV010nohypermut.params.json │ ├── SJETV010nohypermut.ssm │ ├── SJETV010stephR1.params.json │ ├── SJETV010stephR1.ssm │ ├── SJETV010stephR1R2.params.json │ ├── SJETV010stephR1R2.ssm │ ├── SJETV010stephR2.params.json │ ├── SJETV010stephR2.ssm │ ├── SJETV043.params.json │ ├── SJETV043.ssm │ ├── SJETV047.params.json │ ├── SJETV047.ssm │ ├── SJMLL026.params.json │ ├── SJMLL026.ssm │ ├── SJMLL039.params.json │ └── SJMLL039.ssm └── test │ ├── SJtest.handbuilt.json │ ├── SJtest.params.json │ └── SJtest.ssm ├── lib ├── binom.py ├── cluster_linfreq.py ├── cluster_pairwise.py ├── clustermaker.py ├── common.py ├── diversity_indices.py ├── hyperparams.py ├── inputparser.py ├── lh.py ├── lhmath_native.py ├── lhmath_numba.py ├── mutrel.py ├── pairwise.py ├── phi_fitter.py ├── phi_fitter_iterative.py ├── phi_fitter_lol.py ├── phi_fitter_projection.py ├── plotutil.py ├── progressbar.py ├── relation_plotter.py ├── resultserializer.py ├── tree_sampler.py ├── util.py └── vaf_plotter.py ├── misc └── betabinom.py ├── new_math.lyx ├── plot_requirements.txt ├── plot_resources ├── eta_plotter.js ├── highlight_table_labels.js ├── hsluv-0.1.0.min.js ├── matrix.css ├── phi_plotter.js ├── posterior_summ.js ├── tree.css ├── tree_plotter.js ├── util.js └── vaf_matrix.js ├── requirements.txt ├── simulator └── make_simulated_data.sh ├── star_methods ├── methods.params.json ├── methods.ssm └── run_pipeline.sh ├── test_data └── garbage_incorrectly_preferred │ ├── README.md │ ├── examine_demo.png │ ├── mats08.params.json │ ├── mats08.ssm │ └── spawn_repl.patch ├── unused ├── clustermat.py ├── handbuilt.py ├── plot_vaf_matrix.py ├── test_lh.py └── test_phis.py ├── util.cluster └── run_parallel.sh └── util 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