LICENSE
NOTICE
README.md
pyproject.toml
beastxpy/__init__.py
beastxpy/_contracts.py
beastxpy/api.py
beastxpy/assessment.py
beastxpy/calibration.py
beastxpy/capabilities.py
beastxpy/cli_assess.py
beastxpy/cli_capabilities.py
beastxpy/cli_check_data.py
beastxpy/cli_compare.py
beastxpy/cli_container.py
beastxpy/cli_lock.py
beastxpy/cli_report.py
beastxpy/cli_reproduce.py
beastxpy/compare.py
beastxpy/config.py
beastxpy/datacheck.py
beastxpy/diagnostics.py
beastxpy/fragments.py
beastxpy/lockfile.py
beastxpy/main.py
beastxpy/model.py
beastxpy/models.py
beastxpy/partition.py
beastxpy/registry.py
beastxpy/report.py
beastxpy/reproducibility.py
beastxpy/runner.py
beastxpy/sequence.py
beastxpy/tracestats.py
beastxpy/treetools.py
beastxpy/utils.py
beastxpy/validator.py
beastxpy/xml_writer.py
beastxpy.egg-info/PKG-INFO
beastxpy.egg-info/SOURCES.txt
beastxpy.egg-info/dependency_links.txt
beastxpy.egg-info/entry_points.txt
beastxpy.egg-info/requires.txt
beastxpy.egg-info/top_level.txt
beastxpy/coverage/__init__.py
beastxpy/coverage/aa_mixture.py
beastxpy/coverage/ancestral.py
beastxpy/coverage/bdss.py
beastxpy/coverage/beastx_10_5.py
beastxpy/coverage/codon.py
beastxpy/coverage/continuous_trait.py
beastxpy/coverage/discrete_trait.py
beastxpy/coverage/dollo.py
beastxpy/coverage/empirical_tree.py
beastxpy/coverage/mds.py
beastxpy/coverage/mle.py
beastxpy/coverage/recombination.py
beastxpy/coverage/sequence_error.py
beastxpy/coverage/skyride.py
beastxpy/coverage/starbeast.py
beastxpy/data/capabilities.yaml
beastxpy/data/xml_spec.json
beastxpy/tools/BeastXValidator.java
beastxpy/tools/beastx_validate.cmd
beastxpy/tools/beastx_validate.sh
beastxpy/tools/build_jars.py
beastxpy/tools/classes/1.10.4/BeastXValidator.class
beastxpy/tools/classes/1.10.4/bxpshim/BxpShimTreeLikelihoodParser$OldSiteAdapter.class
beastxpy/tools/classes/1.10.4/bxpshim/BxpShimTreeLikelihoodParser$OldSubstAdapter.class
beastxpy/tools/classes/1.10.4/bxpshim/BxpShimTreeLikelihoodParser.class
beastxpy/tools/classes/10.5.0/BeastXValidator.class
beastxpy/tools/classes/10.5.0/bxpshim/BxpShimTreeLikelihoodParser$OldSiteAdapter.class
beastxpy/tools/classes/10.5.0/bxpshim/BxpShimTreeLikelihoodParser$OldSubstAdapter.class
beastxpy/tools/classes/10.5.0/bxpshim/BxpShimTreeLikelihoodParser.class
beastxpy/tools/jars/MANIFEST.txt
beastxpy/tools/jars/beast-1.10.4.jar
beastxpy/tools/jars/beast-10.5.0.jar
beastxpy/tools/java/bxpshim/BxpShimTreeLikelihoodParser.java
beastxpy/tools/parsers/1.10.4/dr/app/beast/devshim_parsers.properties
beastxpy/tools/parsers/10.5.0/dr/app/beast/devshim_parsers.properties
beastxpy/tools/parsers/dr/app/beast/bxpshim_parsers.properties
tests/test_api.py
tests/test_assessment.py
tests/test_auto_priors.py
tests/test_beast_validation.py
tests/test_beauti_reference.py
tests/test_calibration.py
tests/test_capabilities.py
tests/test_cli.py
tests/test_cli_errors.py
tests/test_compare.py
tests/test_config.py
tests/test_config_validation.py
tests/test_container.py
tests/test_coverage_105.py
tests/test_coverage_emp_anc.py
tests/test_coverage_recomb_mds.py
tests/test_coverage_rejections.py
tests/test_coverage_skyride_error.py
tests/test_coverage_traits.py
tests/test_datacheck.py
tests/test_diagnostics.py
tests/test_docs.py
tests/test_fragments.py
tests/test_golden_generation.py
tests/test_lockfile.py
tests/test_model.py
tests/test_numerics.py
tests/test_packaging_integrity.py
tests/test_partition.py
tests/test_prior_families.py
tests/test_properties.py
tests/test_reference_diagnostics.py
tests/test_registry.py
tests/test_release_contract.py
tests/test_report.py
tests/test_reproducibility.py
tests/test_runner.py
tests/test_sequence.py
tests/test_spec_contract.py
tests/test_tracestats.py
tests/test_tracestats_multichain.py
tests/test_treetools.py
tests/test_utils.py
tests/test_validator.py
tests/test_xml_writer.py