CITATION.cff
CITATION.md
CITATION_CN.md
CODE_OF_CONDUCT.md
CODE_OF_CONDUCT_CN.md
CONTRIBUTING.md
CONTRIBUTING_CN.md
LICENSE
MANIFEST.in
QUICKSTART.md
QUICKSTART_CN.md
README.md
README_CN.md
SECURITY.md
SECURITY_CN.md
THIRD_PARTY_LICENSES.md
THIRD_PARTY_LICENSES_CN.md
config.example.yaml
environment.yml
pyproject.toml
requirements.txt
docs/ARCHITECTURE.md
docs/ARCHITECTURE_CN.md
docs/ARCHITECTURE_DECISIONS.md
docs/ARCHITECTURE_DECISIONS_CN.md
docs/CONDA_PACKAGING.md
docs/CONDA_PACKAGING_CN.md
docs/ERROR_CODES.md
docs/ERROR_CODES_CN.md
docs/EXTERNAL_TOOLS.md
docs/EXTERNAL_TOOLS_CN.md
docs/README.md
docs/README_CN.md
docs/TESTING.md
docs/TESTING_CN.md
docs/TEST_RESULTS.md
docs/TEST_RESULTS_CN.md
docs/api/index.rst
docs/api/modules.rst
docs/api/phylodater.adapters.rst
docs/api/phylodater.cli.rst
docs/api/phylodater.core.rst
docs/api/phylodater.infrastructure.rst
docs/api/phylodater.models.rst
docs/api/phylodater.rst
docs/api/phylodater.services.rst
examples/alignment.fasta
examples/calibrations.yaml
examples/checksums.sha256
examples/tree.nwk
examples/truth.yaml
examples/benchmark/degradation/alignment.fasta
examples/benchmark/degradation/calibrations_gamma.yaml
examples/benchmark/degradation/calibrations_uniform.yaml
examples/benchmark/degradation/tree.nwk
examples/benchmark/input/calibrations.yaml
examples/benchmark/input/tree.nwk
examples/benchmark/tier1_manual/lsd2/tree.nwk
examples/benchmark/tier1_manual/treepl/tree.nwk
examples/benchmark/tier1_manual/wlogdate/tree.nwk
phylodater/__init__.py
phylodater/__main__.py
phylodater/_version.py
phylodater/py.typed
phylodater.egg-info/PKG-INFO
phylodater.egg-info/SOURCES.txt
phylodater.egg-info/dependency_links.txt
phylodater.egg-info/entry_points.txt
phylodater.egg-info/requires.txt
phylodater.egg-info/top_level.txt
phylodater/adapters/__init__.py
phylodater/adapters/lsd2_method.py
phylodater/adapters/mcmctree_method.py
phylodater/adapters/mdcat_method.py
phylodater/adapters/pathd8_method.py
phylodater/adapters/r8s_pyr8s_method.py
phylodater/adapters/treepl_method.py
phylodater/adapters/wlogdate_method.py
phylodater/cli/__init__.py
phylodater/cli/main.py
phylodater/core/__init__.py
phylodater/core/batch_processor.py
phylodater/core/comparison_reporter.py
phylodater/core/exceptions.py
phylodater/core/method_interface.py
phylodater/core/pipeline.py
phylodater/infrastructure/__init__.py
phylodater/infrastructure/alignment_metadata.py
phylodater/infrastructure/auto_naming.py
phylodater/infrastructure/checkpoint.py
phylodater/infrastructure/configuration.py
phylodater/infrastructure/container.py
phylodater/infrastructure/logging.py
phylodater/infrastructure/plugins.py
phylodater/infrastructure/process_runner.py
phylodater/infrastructure/runtime_metadata.py
phylodater/infrastructure/safe_io.py
phylodater/infrastructure/self_test.py
phylodater/infrastructure/signal_handler.py
phylodater/infrastructure/software_dependencies.py
phylodater/models/__init__.py
phylodater/models/calibration.py
phylodater/models/constraints.py
phylodater/models/results.py
phylodater/models/tree.py
phylodater/services/__init__.py
phylodater/services/auto_calibrator.py
phylodater/services/calibration_loader.py
phylodater/services/calibration_resolver.py
phylodater/services/deep_validator.py
phylodater/services/input_validator.py
phylodater/services/name_mapping.py
phylodater/services/taxonomy_parser.py
phylodater/services/tree_rooting.py
phylodater/services/tree_validator.py
phylodater/viz/__init__.py
phylodater/viz/backends.py
phylodater/viz/dating_figure.py
phylodater/viz/geo_plot.py
phylodater/viz/tree_plot.py
phylodater/viz/data/__init__.py
phylodater/viz/data/ics_timescale.csv
scripts/check_docs.py
scripts/degradation_experiment.py
scripts/generate_checksums.py
scripts/probe_pyr8s_constraints.py
scripts/run_reference_benchmark.py
scripts/tier1_manual_comparison.py
test-data/README.md
test-data/README_CN.md
test-data/benchmark/alignment.fasta
test-data/benchmark/calibrations.yaml
test-data/benchmark/checksums.sha256
test-data/benchmark/generate_benchmark_dataset.py
test-data/benchmark/tree.nwk
test-data/benchmark/tree_ml.nwk
test-data/benchmark/truth.yaml
test-data/benchmark/results/PYTHON_SUPPORT_MATRIX.txt
test-data/benchmark/results/benchmark_results.json
test-data/benchmark/results/node_ages.tsv
test-data/benchmark/results/scorecard.tsv
test-data/benchmark/results/validation_log.txt
test-data/benchmark/results/ml_tree/benchmark_results.json
test-data/benchmark/results/ml_tree/node_ages.tsv
test-data/benchmark/results/ml_tree/scorecard.tsv
test-data/input/boundary/bom_tree.nwk
test-data/input/boundary/empty_tree.nwk
test-data/input/boundary/gbk_tree.nwk
test-data/input/boundary/multiple_trees.nex
test-data/input/invalid/circular_taxonomy.tsv
test-data/input/invalid/control_char_tree.nwk
test-data/input/invalid/duplicate_internal_labels.nwk
test-data/input/invalid/duplicate_leaf_names.nwk
test-data/input/invalid/duplicate_seq_id.fasta
test-data/input/invalid/empty_alignment.fasta
test-data/input/invalid/invalid_dna_chars.fasta
test-data/input/invalid/invalid_uniform.yaml
test-data/input/invalid/invalid_yaml.yaml
test-data/input/invalid/negative_branch_tree.nwk
test-data/input/invalid/phylip_format.phy
test-data/input/invalid/unbalanced_tree.nwk
test-data/input/invalid/unicode_bidi_tree.nwk
test-data/input/invalid/zero_width_tree.nwk
test-data/input/valid/alignment.fasta
test-data/input/valid/calibrations.yaml
test-data/input/valid/tree.nwk
tests/__init__.py
tests/conftest.py
tests/fixtures/__init__.py
tests/fixtures/data_generator.py
tests/fixtures/test_data/__init__.py
tests/functional/__init__.py
tests/functional/conftest.py
tests/functional/test_adapters.py
tests/functional/test_batch_checkpoint.py
tests/functional/test_calibration.py
tests/functional/test_cli.py
tests/functional/test_input_validation.py
tests/functional/test_pipeline.py
tests/functional/test_report.py
tests/functional/test_security.py
tests/functional/test_self_check.py
tests/functional/test_signals.py
tests/functional/test_taxonomy.py
tests/functional/test_visualization.py
tests/integration/__init__.py
tests/integration/test_pipeline_integration.py
tests/integration/full_pipeline/__init__.py
tests/integration/full_pipeline/generate_beautiful_tree.py
tests/integration/full_pipeline/test_all_dating_tools.py
tests/integration/full_pipeline/test_pipeline_flow.py
tests/integration/full_pipeline/test_visualization.py
tests/unit/__init__.py
tests/unit/test_review_fixes.py
tests/unit/test_viz_geo.py
tests/unit/adapters/__init__.py
tests/unit/adapters/test_lsd2_method.py
tests/unit/adapters/test_mcmctree_convergence.py
tests/unit/adapters/test_mcmctree_method.py
tests/unit/adapters/test_mcmctree_rate_estimation.py
tests/unit/adapters/test_mdcat_method.py
tests/unit/adapters/test_pathd8_method.py
tests/unit/adapters/test_r8s_pyr8s_method.py
tests/unit/adapters/test_treepl_method.py
tests/unit/adapters/test_wlogdate_method.py
tests/unit/cli/__init__.py
tests/unit/cli/test_input_validation.py
tests/unit/core/__init__.py
tests/unit/core/test_exceptions.py
tests/unit/core/test_method_interface.py
tests/unit/core/test_pipeline.py
tests/unit/infrastructure/__init__.py
tests/unit/infrastructure/test_configuration.py
tests/unit/infrastructure/test_memory_handling.py
tests/unit/infrastructure/test_process_runner.py
tests/unit/infrastructure/test_safe_io.py
tests/unit/infrastructure/test_software_dependencies.py
tests/unit/models/__init__.py
tests/unit/models/test_constraints.py
tests/unit/models/test_constraints_render.py
tests/unit/models/test_tree.py
tests/unit/services/__init__.py
tests/unit/services/test_calibration_loader.py
tests/unit/services/test_calibration_resolver.py
tests/unit/services/test_deep_validator.py
tests/unit/services/test_name_mapping.py
tests/unit/services/test_taxonomy_parser.py
tests/unit/services/test_tree_rooting.py
tests/unit/services/test_tree_validator.py
tests/validation/__init__.py
tests/validation/conftest.py
tests/validation/helpers.py
tests/validation/adapters/__init__.py
tests/validation/adapters/test_adapter_interface.py
tests/validation/adapters/test_mcmctree.py
tests/validation/adapters/test_other_adapters.py
tests/validation/fixtures/__init__.py
tests/validation/fixtures/alignments/duplicate_id.fasta
tests/validation/fixtures/alignments/mismatched.fasta
tests/validation/fixtures/alignments/protein_sample.fasta
tests/validation/fixtures/alignments/small_sample.fasta
tests/validation/fixtures/alignments/small_tree.fasta
tests/validation/fixtures/alignments/taxonomy_tree.fasta
tests/validation/fixtures/benchmark/alignment.fasta
tests/validation/fixtures/benchmark/calibrations.yaml
tests/validation/fixtures/benchmark/tree.nwk
tests/validation/fixtures/calibrations/all_types.yaml
tests/validation/fixtures/calibrations/empty.yaml
tests/validation/fixtures/calibrations/missing_type.yaml
tests/validation/fixtures/calibrations/nan_age.yaml
tests/validation/fixtures/calibrations/pathd8_fixed.yaml
tests/validation/fixtures/calibrations/root_only.yaml
tests/validation/fixtures/calibrations/small_tree_uniform.yaml
tests/validation/fixtures/calibrations/taxonomy_tree.yaml
tests/validation/fixtures/calibrations/valid_fixed.yaml
tests/validation/fixtures/calibrations/valid_soft_bounds.yaml
tests/validation/fixtures/calibrations/valid_uniform.yaml
tests/validation/fixtures/configs/custom_threads.yaml
tests/validation/fixtures/configs/default.yaml
tests/validation/fixtures/taxonomies/taxonomy.tsv
tests/validation/fixtures/taxonomies/taxonomy_mismatched.tsv
tests/validation/fixtures/taxonomies/taxonomy_multicol.tsv
tests/validation/fixtures/trees/empty.nwk
tests/validation/fixtures/trees/example_tree.nwk
tests/validation/fixtures/trees/malicious_tree.nwk
tests/validation/fixtures/trees/medium_sample.nwk
tests/validation/fixtures/trees/negative_branch.nwk
tests/validation/fixtures/trees/small_sample.nwk
tests/validation/fixtures/trees/taxonomy_tree.nwk
tests/validation/fixtures/trees/unrooted_sample.nwk
tests/validation/fixtures/trees/with_internal_labels.nwk
tests/validation/functional/__init__.py
tests/validation/functional/test_auto_calibrate.py
tests/validation/functional/test_cli_check.py
tests/validation/functional/test_cli_dating.py
tests/validation/functional/test_cli_errors.py
tests/validation/functional/test_cli_fold.py
tests/validation/functional/test_pipeline_dry_run.py
tests/validation/integration/__init__.py
tests/validation/integration/test_all_dating_tools.py
tests/validation/integration/test_checkpoint_resume.py
tests/validation/integration/test_end_to_end_mcmctree.py
tests/validation/integration/test_multi_method.py
tests/validation/security/__init__.py
tests/validation/security/test_input_safety.py
tests/validation/security/test_path_traversal.py
tests/validation/security/test_yaml_safety.py
tests/validation/unit/__init__.py
tests/validation/unit/test_calibration_loader.py
tests/validation/unit/test_calibration_models.py
tests/validation/unit/test_calibration_resolver.py
tests/validation/unit/test_checkpoint.py
tests/validation/unit/test_configuration.py
tests/validation/unit/test_input_validator.py
tests/validation/unit/test_logging.py
tests/validation/unit/test_method_registry.py
tests/validation/unit/test_pipeline_config.py
tests/validation/unit/test_taxonomy_parser.py
tests/validation/unit/test_tree_model.py
tests/validation/unit/test_tree_rooting.py
tests/validation/unit/test_tree_topology.py