.flake8
CITATION.cff
LICENSE
MANIFEST.in
README.md
README_zh.md
beast2_validate.sh
pyproject.toml
beast2py/__init__.py
beast2py/api.py
beast2py/beast2_validate.sh
beast2py/calibration.py
beast2py/config.py
beast2py/diagnostics.py
beast2py/main.py
beast2py/model.py
beast2py/models.py
beast2py/partition.py
beast2py/registry.py
beast2py/reproducibility.py
beast2py/sequence.py
beast2py/utils.py
beast2py/validator.py
beast2py/xml_writer.py
beast2py.egg-info/PKG-INFO
beast2py.egg-info/SOURCES.txt
beast2py.egg-info/dependency_links.txt
beast2py.egg-info/entry_points.txt
beast2py.egg-info/requires.txt
beast2py.egg-info/top_level.txt
beast2py/tools/Beast2Validator.java
beast2py/tools/LICENSE.BEAST2-LGPL-2.1.txt
beast2py/tools/NOTICE
beast2py/tools/launcher.jar
beast2py/tools/classes/Beast2Validator.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$ArgumentException.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$IntegerArrayOption.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$IntegerOption.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$LongOption.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$Option.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$RealArrayOption.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$RealOption.class
beast2py/tools/classes/beast/pkgmgmt/Arguments$StringOption.class
beast2py/tools/classes/beast/pkgmgmt/Arguments.class
beast2py/tools/classes/beast/pkgmgmt/BEASTClassLoader.class
beast2py/tools/classes/beast/pkgmgmt/BEASTVersion.class
beast2py/tools/classes/beast/pkgmgmt/MultiParentURLClassLoader.class
beast2py/tools/classes/beast/pkgmgmt/Package.class
beast2py/tools/classes/beast/pkgmgmt/PackageDependency.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$1.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$2.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$3.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$4.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$5.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$6.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$7.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$8.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$DependencyResolutionException.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$PackageListRetrievalException.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager$UpdateStatus.class
beast2py/tools/classes/beast/pkgmgmt/PackageManager.class
beast2py/tools/classes/beast/pkgmgmt/PackageVersion.class
beast2py/tools/classes/beast/pkgmgmt/Utils6$Canvas.class
beast2py/tools/classes/beast/pkgmgmt/Utils6.class
beast2py/tools/classes/beast/pkgmgmt/Version.class
docs/architecture_en.md
docs/architecture_zh.md
docs/calibration_guide_en.md
docs/calibration_guide_zh.md
docs/tutorial_en.md
docs/tutorial_zh.md
docs/user_manual_en.md
docs/user_manual_zh.md
docs/xml_format_en.md
docs/xml_format_zh.md
examples/aminoacid.fasta
examples/calibrations.yaml
examples/config_aa_jtt.yaml
examples/config_aa_model.yaml
examples/config_advanced.yaml
examples/config_basic.yaml
examples/config_bd_skyline.yaml
examples/config_calibrated_yule.yaml
examples/config_coalescent_exponential.yaml
examples/config_ebsp.yaml
examples/config_multi_partition.yaml
examples/config_nested_sampling.yaml
examples/config_relaxed_clock.yaml
examples/config_relaxed_exponential.yaml
examples/config_rlc.yaml
examples/config_skyline.yaml
examples/config_subst_jc69.yaml
examples/config_subst_models.yaml
examples/config_subst_sym.yaml
examples/config_subst_tim.yaml
examples/config_tip_dates.yaml
examples/output_basic.fingerprint.json
examples/output_basic.methods.tex
examples/output_basic.xml
examples/primates.fasta
tests/__init__.py
tests/conftest.py
tests/test_beast2_validation.py
tests/test_calibration.py
tests/test_cli.py
tests/test_config.py
tests/test_diagnostics.py
tests/test_model.py
tests/test_partition.py
tests/test_release_integrity.py
tests/test_reproducibility.py
tests/test_semantic_invariants.py
tests/test_sequence.py
tests/test_utils.py
tests/test_validator.py
tests/test_xml_types.py
tests/test_xml_writer.py