LICENSE
README.md
pyproject.toml
src/beast_pype/COVID.py
src/beast_pype/__init__.py
src/beast_pype/beast_xml_gen.py
src/beast_pype/cli.py
src/beast_pype/date_utilities.py
src/beast_pype/fig_utils.py
src/beast_pype/nb_utils.py
src/beast_pype/outputs.py
src/beast_pype/path_utils.py
src/beast_pype/report_gen.py
src/beast_pype/seq_samplers.py
src/beast_pype/stat_distributions.py
src/beast_pype/tree_time_scale.py
src/beast_pype/workflow_params.py
src/beast_pype.egg-info/PKG-INFO
src/beast_pype.egg-info/SOURCES.txt
src/beast_pype.egg-info/dependency_links.txt
src/beast_pype.egg-info/entry_points.txt
src/beast_pype.egg-info/requires.txt
src/beast_pype.egg-info/top_level.txt
src/beast_pype/diagnostics/__init__.py
src/beast_pype/diagnostics/gen_diag_nb.py
src/beast_pype/diagnostics/mcmc.py
src/beast_pype/diagnostics/runtime.py
src/beast_pype/report_templates/BDSKY-Serial-Comparative.ipynb
src/beast_pype/report_templates/BDSKY-Serial.ipynb
src/beast_pype/report_templates/COVID-Strain-Surveillance.ipynb
src/beast_pype/report_templates/Generic-Comparative.ipynb
src/beast_pype/report_templates/Generic.ipynb
src/beast_pype/report_templates/__init__.py
src/beast_pype/workflow_modules/Phase-1-Metadata-and-Sequence-Separation.ipynb
src/beast_pype/workflow_modules/Phase-2i-and-2iii-IQTree-Building.ipynb
src/beast_pype/workflow_modules/Phase-2i-and-2iii-IQTree-Correction.ipynb
src/beast_pype/workflow_modules/Phase-2ii-and-2iv-TreeTime-and-Downsampling.ipynb
src/beast_pype/workflow_modules/Phase-3-Gen-BDSKY-Serial-xml.ipynb
src/beast_pype/workflow_modules/Phase-3-Gen-Generic-xml.ipynb
src/beast_pype/workflow_modules/Phase-4-GNU-Parallel-Running-BEAST.ipynb
src/beast_pype/workflow_modules/Phase-4-SBATCH-Running-BEAST.ipynb
src/beast_pype/workflow_modules/Phase-5-Diagnosing-Outputs-and-Generate-Report.ipynb
src/beast_pype/workflow_modules/Phase-5-Diagnosing-Runtime-and-Resource-Usage.ipynb
src/beast_pype/workflow_modules/Phase-5-Diagnosing-XML-sets-and-Generate-Report.ipynb
src/beast_pype/workflow_modules/Phase-5i-Merge-BEAST-outputs.ipynb
src/beast_pype/workflow_modules/Phase-5ii-Gen-MCC-Trees.ipynb
src/beast_pype/workflow_modules/__init__.py
src/beast_pype/workflows/BDSKY-Serial-Comparative.ipynb
src/beast_pype/workflows/BDSKY-Serial.ipynb
src/beast_pype/workflows/COVID-Strain-Surveillance.ipynb
src/beast_pype/workflows/Generic-Comparative.ipynb
src/beast_pype/workflows/Generic.ipynb
src/beast_pype/workflows/Optimising-BEAST-Runs.ipynb
src/beast_pype/workflows/__init__.py
tests/test_BDSKY-Serial-Comparative.py
tests/test_BDSKY-Serial_workflow.py
tests/test_COVID-Strain-Surveillance.py
tests/test_Generic-Comparative_workflow.py
tests/test_Generic_workflow.py