LICENSE
MANIFEST.in
README.md
pyproject.toml
examples/v1_tiny_orthofinder/Pfam-A.hmm.dat
examples/v1_tiny_orthofinder/README.md
examples/v1_tiny_orthofinder/count_matrix.tsv
examples/v1_tiny_orthofinder/covariance.tsv
examples/v1_tiny_orthofinder/pfam.domtblout
examples/v1_tiny_orthofinder/proteins.faa
examples/v1_tiny_orthofinder/species.txt
examples/v1_tiny_orthofinder/species_tree.nwk
examples/v1_tiny_orthofinder/traits.csv
examples/v1_tiny_orthofinder/OrthoFinder/Results/Orthogroups/Orthogroups.GeneCount.tsv
examples/v1_tiny_orthofinder/OrthoFinder/Results/Orthogroups/Orthogroups.tsv
examples/v1_tiny_orthofinder/OrthoFinder/Results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv
orthoglmm/__init__.py
orthoglmm/calibrate_artifacts.py
orthoglmm/calibrate_cli.py
orthoglmm/calibrate_config.py
orthoglmm/calibrate_diagnostics.py
orthoglmm/calibrate_io.py
orthoglmm/calibrate_predictors.py
orthoglmm/calibrate_pvals.py
orthoglmm/calibrate_results.py
orthoglmm/calibrate_results_cli.py
orthoglmm/calibrate_score_fields.py
orthoglmm/calibrate_solver_apply.py
orthoglmm/calibrate_solver_fit_chunk.py
orthoglmm/calibrate_solver_fit_metadata.py
orthoglmm/calibrate_solver_metadata.py
orthoglmm/calibrate_solver_nulls.py
orthoglmm/calibrate_solver_state.py
orthoglmm/calibrate_solver_tasks.py
orthoglmm/calibrate_state.py
orthoglmm/cli_filter_verify.py
orthoglmm/concat_inference.py
orthoglmm/concat_main.py
orthoglmm/concat_nodes.py
orthoglmm/concat_results.py
orthoglmm/concat_rows.py
orthoglmm/count_matrix_io.py
orthoglmm/dating.py
orthoglmm/elastic_phylo.py
orthoglmm/feature_matrix.py
orthoglmm/gene_trees.py
orthoglmm/matrix_store.py
orthoglmm/merge_parquet.py
orthoglmm/meta_families.py
orthoglmm/mode_labels.py
orthoglmm/node_scan.py
orthoglmm/node_scan_cli.py
orthoglmm/node_scan_data.py
orthoglmm/node_scan_engine.py
orthoglmm/node_scan_fit.py
orthoglmm/node_scan_nulls.py
orthoglmm/node_scan_results.py
orthoglmm/node_scan_run_api.py
orthoglmm/node_scan_runner.py
orthoglmm/node_scan_scan_api.py
orthoglmm/node_scan_screen.py
orthoglmm/node_scan_types.py
orthoglmm/null_calibration.py
orthoglmm/null_covariance.py
orthoglmm/null_simulation.py
orthoglmm/nulls.py
orthoglmm/orthofinder_discovery.py
orthoglmm/orthofinder_features.py
orthoglmm/permutation.py
orthoglmm/pfam_annotation.py
orthoglmm/phylo_precision.py
orthoglmm/pipeline.py
orthoglmm/pipeline_cli.py
orthoglmm/pipeline_io.py
orthoglmm/predictors.py
orthoglmm/prepare_data_cli.py
orthoglmm/print_top_candidates.py
orthoglmm/provenance.py
orthoglmm/qq_plots.py
orthoglmm/reconciliation.py
orthoglmm/result_json.py
orthoglmm/result_summary.py
orthoglmm/ridge_solver_rows.py
orthoglmm/run_ridge_solver_cli.py
orthoglmm/runtime.py
orthoglmm/scan_fingerprints.py
orthoglmm/script_entrypoint.py
orthoglmm/sequence_triage.py
orthoglmm/sequence_triage_cli.py
orthoglmm/sequence_triage_core.py
orthoglmm/smoke.py
orthoglmm/solver_cli.py
orthoglmm/solver_config.py
orthoglmm/solver_core.py
orthoglmm/solver_elastic.py
orthoglmm/solver_fallback.py
orthoglmm/solver_finalize.py
orthoglmm/solver_firth.py
orthoglmm/solver_fit.py
orthoglmm/solver_inference.py
orthoglmm/solver_io.py
orthoglmm/solver_optim.py
orthoglmm/solver_output.py
orthoglmm/solver_pql.py
orthoglmm/solver_robust.py
orthoglmm/solver_runner.py
orthoglmm/solver_screen.py
orthoglmm/solver_smoke.py
orthoglmm/solver_types.py
orthoglmm/solver_utils.py
orthoglmm/species_labels.py
orthoglmm/statistics.py
orthoglmm/task_manifest.py
orthoglmm/tools.py
orthoglmm/tools_calibration.py
orthoglmm/tools_config.py
orthoglmm/tools_doctor.py
orthoglmm/tools_meta.py
orthoglmm/tools_null_depth.py
orthoglmm/tools_parser.py
orthoglmm/tools_scan.py
orthoglmm/tools_summary.py
orthoglmm/tools_tasks.py
orthoglmm/tools_trait.py
orthoglmm/tools_tree.py
orthoglmm/trait_io.py
orthoglmm/verify_temporal.py
orthoglmm.egg-info/PKG-INFO
orthoglmm.egg-info/SOURCES.txt
orthoglmm.egg-info/dependency_links.txt
orthoglmm.egg-info/entry_points.txt
orthoglmm.egg-info/requires.txt
orthoglmm.egg-info/top_level.txt
orthoglmm/phylo_relatedness/__init__.py
orthoglmm/phylo_relatedness/phylo_relatedness.py
orthoglmm_script_impl/__init__.py
orthoglmm_script_impl/calibrate.py
orthoglmm_script_impl/classify_toolkits.py
orthoglmm_script_impl/prep_amr_data.py
orthoglmm_script_impl/prepare_data.py
orthoglmm_script_impl/run_elastic_solver.py
orthoglmm_script_impl/run_pipeline.py
orthoglmm_script_impl/run_ridge_solver.py
orthoglmm_script_impl/run_solver_on_real_data.py
orthoglmm_script_impl/trace_swissprot_candidates.py
orthoglmm_script_impl/verify_candidates.py
tests/test_bench_laplace.py
tests/test_calibrate.py
tests/test_calibrate_artifacts_predictors_script.py
tests/test_calibrate_helpers_script.py
tests/test_calibrate_io.py
tests/test_calibrate_predictors.py
tests/test_calibrate_pvals.py
tests/test_calibrate_results.py
tests/test_calibrate_score_fields.py
tests/test_calibrate_script.py
tests/test_calibrate_solver_apply.py
tests/test_calibrate_solver_fit_chunk.py
tests/test_calibrate_solver_fit_metadata.py
tests/test_calibrate_solver_metadata.py
tests/test_calibrate_solver_nulls.py
tests/test_calibrate_solver_permutation_script.py
tests/test_calibrate_solver_state.py
tests/test_calibrate_solver_state_script.py
tests/test_calibrate_solver_tasks.py
tests/test_calibrate_state.py
tests/test_classify_toolkits.py
tests/test_cleanup_coverage_helpers.py
tests/test_cli_filter_verify.py
tests/test_cli_improvements.py
tests/test_concat_nodes.py
tests/test_concat_results.py
tests/test_concat_results_cli.py
tests/test_concat_results_hypothesis.py
tests/test_concat_results_more_hypothesis.py
tests/test_concat_results_no_nodes.py
tests/test_concat_stats.py
tests/test_count_matrix_io.py
tests/test_date_trait_origins_script.py
tests/test_dating.py
tests/test_elastic_on_simulated_data.py
tests/test_elastic_phylo.py
tests/test_feature_matrix.py
tests/test_firth_statsmodels.py
tests/test_generate_predictors_from_tree.py
tests/test_hypothesis_properties.py
tests/test_laplace_small_n.py
tests/test_math_utils.py
tests/test_matrix_store.py
tests/test_merge_parquet.py
tests/test_meta_families.py
tests/test_node_scan.py
tests/test_node_scan_cli.py
tests/test_node_scan_data.py
tests/test_nulls.py
tests/test_nulls_calibrator.py
tests/test_nulls_hypothesis.py
tests/test_orthofinder_discovery.py
tests/test_orthofinder_features.py
tests/test_permutation.py
tests/test_pfam_annotation.py
tests/test_phylo_precision.py
tests/test_pipeline.py
tests/test_pipeline_cli.py
tests/test_pipeline_io.py
tests/test_pipeline_io_helpers.py
tests/test_pipeline_io_hypothesis.py
tests/test_pipeline_io_load_data.py
tests/test_pipeline_io_prep_bundle.py
tests/test_pipeline_matrix_mode.py
tests/test_predictors.py
tests/test_prep_amr_data.py
tests/test_prep_tree.py
tests/test_prepare_data.py
tests/test_provenance.py
tests/test_qq_plots.py
tests/test_qq_plots_columns.py
tests/test_qq_plots_hypothesis.py
tests/test_reconciliation.py
tests/test_result_json.py
tests/test_run_amr_solver.py
tests/test_run_elastic_solver.py
tests/test_run_pipeline.py
tests/test_run_pipeline_wrapper.py
tests/test_run_ridge_solver.py
tests/test_run_ridge_solver_io_helpers.py
tests/test_run_ridge_solver_matrix_helpers.py
tests/test_run_ridge_solver_response_helpers.py
tests/test_run_ridge_solver_reverse_cli.py
tests/test_run_solver_on_real_data_impl.py
tests/test_runtime.py
tests/test_sequence_triage.py
tests/test_sequence_triage_cli.py
tests/test_sequence_triage_core.py
tests/test_solver.py
tests/test_solver_cli.py
tests/test_solver_config.py
tests/test_solver_core.py
tests/test_solver_elastic.py
tests/test_solver_elastic_more.py
tests/test_solver_fallback.py
tests/test_solver_fallback_more.py
tests/test_solver_finalize.py
tests/test_solver_firth.py
tests/test_solver_fit.py
tests/test_solver_glmm_properties.py
tests/test_solver_hypothesis.py
tests/test_solver_inference.py
tests/test_solver_io.py
tests/test_solver_matrix_mode.py
tests/test_solver_optim.py
tests/test_solver_output.py
tests/test_solver_pql.py
tests/test_solver_pql_more_hypothesis.py
tests/test_solver_robust.py
tests/test_solver_robust_more.py
tests/test_solver_runner.py
tests/test_solver_screen.py
tests/test_solver_types.py
tests/test_solver_utils.py
tests/test_solver_utils_cache.py
tests/test_statistical_correctness_guards.py
tests/test_statistics.py
tests/test_statistics_evidence.py
tests/test_statistics_extra.py
tests/test_statistics_hypothesis_batch.py
tests/test_statistics_more_edges.py
tests/test_summarize_candidates.py
tests/test_summarize_result_hypothesis.py
tests/test_temporal_concordance.py
tests/test_tools.py
tests/test_tools_misc_commands.py
tests/test_tools_node_sequence.py
tests/test_tools_task_manifest.py
tests/test_tools_tree.py
tests/test_tools_tree_commands.py
tests/test_tools_uniform_pvalues_hypothesis.py
tests/test_trace_swissprot_candidates.py
tests/test_v1_example_dataset.py
tests/test_validate_count_matrix.py
tests/test_verify_candidates.py