CHANGELOG-zh.md
CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README-zh.md
README.md
THIRD-PARTY-NOTICES-zh.md
THIRD-PARTY-NOTICES.md
pyproject.toml
data/PROVENANCE-zh.md
data/PROVENANCE.md
data/examples/README-zh.md
data/examples/README.md
data/examples/example.nwk
data/examples/example_calibrations.tsv
data/examples/example_calibrations_feasible.tsv
data/examples/example_taxa.tsv
data/golden/r3f/example_RRF_rates.csv
data/golden/r3f/example_RRF_rates.nwk
data/golden/r3f/example_RRF_table.csv
data/golden/r3f/example_RRF_times.csv
data/golden/r3f/example_RRF_timetree.nexus
data/golden/r3f/example_RRF_timetree.nwk
data/golden/r3f/example_anchor_ddbd.txt
data/golden/r3f/example_corrtest_full_precision.txt
data/golden/r3f/example_noanchor_ddbd.txt
data/golden/r3f/example_rooted_dropped.nwk
data/golden/r3f/example_sr0_corrtest.txt
data/golden/r3f/example_sr50_corrtest.txt
data/golden/r3f/example_tree2table.csv
docs/README.md
docs/methods-zh.md
docs/methods.md
docs/parameters-zh.md
docs/parameters.md
docs/usage-en.md
docs/usage-zh.md
docs/validation-zh.md
docs/validation.md
docs/adr/ADR-004-tree-operations-zh.md
docs/adr/ADR-004-tree-operations.md
docs/adr/README-zh.md
docs/adr/README.md
docs/tutorials/tutorial1-quickstart-zh.md
docs/tutorials/tutorial1-quickstart.md
docs/tutorials/tutorial2-end-to-end-zh.md
docs/tutorials/tutorial2-end-to-end.md
docs/tutorials/tutorial3-priors-megacc-zh.md
docs/tutorials/tutorial3-priors-megacc.md
e2e_tests/README-zh.md
e2e_tests/README.md
e2e_tests/TEST_PLAN-zh.md
e2e_tests/TEST_PLAN.md
e2e_tests/conftest.py
e2e_tests/cases/test_01_rrf_core.py
e2e_tests/cases/test_02_calibration_ci.py
e2e_tests/cases/test_03_corrtest_ddbd.py
e2e_tests/cases/test_04_tree2table_monophyly.py
e2e_tests/cases/test_05_cli_api_parity.py
e2e_tests/cases/test_06_input_validation.py
e2e_tests/cases/test_07_blb_external.py
e2e_tests/cases/test_08_megacc_external.py
e2e_tests/data/example.fasta
e2e_tests/data/example.nwk
e2e_tests/data/example_calibrations.tsv
e2e_tests/data/example_taxa.tsv
e2e_tests/data/small.fasta
e2e_tests/data/golden/example_RRF_rates.csv
e2e_tests/data/golden/example_RRF_rates.nwk
e2e_tests/data/golden/example_RRF_table.csv
e2e_tests/data/golden/example_RRF_times.csv
e2e_tests/data/golden/example_RRF_timetree.nexus
e2e_tests/data/golden/example_RRF_timetree.nwk
e2e_tests/data/golden/example_anchor_ddbd.txt
e2e_tests/data/golden/example_corrtest_full_precision.txt
e2e_tests/data/golden/example_noanchor_ddbd.txt
e2e_tests/data/golden/example_rooted_dropped.nwk
e2e_tests/data/golden/example_sr0_corrtest.txt
e2e_tests/data/golden/example_sr50_corrtest.txt
e2e_tests/data/golden/example_tree2table.csv
figures/README.md
figures/make_figures.py
figures/附件图S1-软件架构图.py
figures/附件图S2-性能对比图-data.json
figures/附件图S2-性能对比图.py
figures/附件图S3-置信区间图-data.json
figures/附件图S3-置信区间图.py
openreltime/__init__.py
openreltime/_constants.py
openreltime/_external.py
openreltime/bootstrap.py
openreltime/calibrate.py
openreltime/ci.py
openreltime/cli.py
openreltime/corrtest.py
openreltime/ddbd.py
openreltime/megacc.py
openreltime/rates.py
openreltime/report.py
openreltime/rrf.py
openreltime/table.py
openreltime/taxonomy.py
openreltime/times.py
openreltime/tree.py
openreltime/treeio.py
openreltime/viz.py
openreltime.egg-info/PKG-INFO
openreltime.egg-info/SOURCES.txt
openreltime.egg-info/dependency_links.txt
openreltime.egg-info/entry_points.txt
openreltime.egg-info/requires.txt
openreltime.egg-info/top_level.txt
reproduce/golden_r3f.R
reproduce/golden_r3f_fullprec.R
tests/test_calibration_ci_edges.py
tests/test_g1_hand_computed.py
tests/test_regression_golden.py
tests/test_regressions_calibration_ci.py
tests/test_regressions_engine.py
tests/test_regressions_rrf_engine.py
tests/test_regressions_treeio_peripherals.py
tests/test_taxonomy_monophyly.py