README.md
pyproject.toml
bella_companion/BELLA.jar
bella_companion/__init__.py
bella_companion/cli.py
bella_companion/version.xml
bella_companion.egg-info/PKG-INFO
bella_companion.egg-info/SOURCES.txt
bella_companion.egg-info/dependency_links.txt
bella_companion.egg-info/entry_points.txt
bella_companion.egg-info/requires.txt
bella_companion.egg-info/top_level.txt
bella_companion/__pycache__/__init__.cpython-310.pyc
bella_companion/__pycache__/cli.cpython-310.pyc
bella_companion/eucovid/__init__.py
bella_companion/eucovid/run_beast.py
bella_companion/eucovid/__pycache__/__init__.cpython-310.pyc
bella_companion/eucovid/__pycache__/run_beast.cpython-310.pyc
bella_companion/eucovid/beast_configs/GLM.xml
bella_companion/eucovid/beast_configs/MLP.xml
bella_companion/eucovid/beast_configs/Nonparametric.xml
bella_companion/eucovid/data/case_data.tsv
bella_companion/eucovid/data/change_dates.tsv
bella_companion/eucovid/data/msa.fasta
bella_companion/eucovid/data/osi.tsv
bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv
bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv
bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv
bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv
bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv
bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv
bella_companion/platyrrhine/__init__.py
bella_companion/platyrrhine/beast_config.xml
bella_companion/platyrrhine/results.py
bella_companion/platyrrhine/run_beast.py
bella_companion/platyrrhine/summarize.py
bella_companion/platyrrhine/__pycache__/__init__.cpython-310.pyc
bella_companion/platyrrhine/__pycache__/results.cpython-310.pyc
bella_companion/platyrrhine/__pycache__/run_beast.cpython-310.pyc
bella_companion/platyrrhine/__pycache__/summarize.cpython-310.pyc
bella_companion/platyrrhine/__pycache__/summarize_logs.cpython-310.pyc
bella_companion/platyrrhine/data/change_times.csv
bella_companion/platyrrhine/data/traits.csv
bella_companion/platyrrhine/data/trees.nwk
bella_companion/simulations/__init__.py
bella_companion/simulations/features.py
bella_companion/simulations/generate_data.py
bella_companion/simulations/generate_figures.py
bella_companion/simulations/metrics.py
bella_companion/simulations/run_beast.py
bella_companion/simulations/summarize.py
bella_companion/simulations/__pycache__/__init__.cpython-310.pyc
bella_companion/simulations/__pycache__/features.cpython-310.pyc
bella_companion/simulations/__pycache__/generate_data.cpython-310.pyc
bella_companion/simulations/__pycache__/generate_figures.cpython-310.pyc
bella_companion/simulations/__pycache__/metrics.cpython-310.pyc
bella_companion/simulations/__pycache__/run_beast.cpython-310.pyc
bella_companion/simulations/__pycache__/summarize.cpython-310.pyc
bella_companion/simulations/__pycache__/summarize_logs.cpython-310.pyc
bella_companion/simulations/beast_configs/epi-multitype/GLM.xml
bella_companion/simulations/beast_configs/epi-multitype/MLP.xml
bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml
bella_companion/simulations/beast_configs/epi-skyline/GLM.xml
bella_companion/simulations/beast_configs/epi-skyline/MLP.xml
bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml
bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml
bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml
bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml
bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml
bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml
bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml
bella_companion/simulations/figures/__init__.py
bella_companion/simulations/figures/epi_multitype.py
bella_companion/simulations/figures/epi_skyline.py
bella_companion/simulations/figures/fbd_2traits.py
bella_companion/simulations/figures/fbd_no_traits.py
bella_companion/simulations/figures/scenarios.py
bella_companion/simulations/figures/utils.py
bella_companion/simulations/figures/__pycache__/__init__.cpython-310.pyc
bella_companion/simulations/figures/__pycache__/epi_multitype.cpython-310.pyc
bella_companion/simulations/figures/__pycache__/epi_skyline.cpython-310.pyc
bella_companion/simulations/figures/__pycache__/fbd_2traits.cpython-310.pyc
bella_companion/simulations/figures/__pycache__/fbd_no_traits.cpython-310.pyc
bella_companion/simulations/figures/__pycache__/scenarios.cpython-310.pyc
bella_companion/simulations/figures/__pycache__/utils.cpython-310.pyc
bella_companion/simulations/figures/explain/__init__.py
bella_companion/simulations/figures/explain/pdp.py
bella_companion/simulations/figures/explain/shap.py
bella_companion/simulations/figures/explain/__pycache__/__init__.cpython-310.pyc
bella_companion/simulations/figures/explain/__pycache__/pdp.cpython-310.pyc
bella_companion/simulations/figures/explain/__pycache__/shap.cpython-310.pyc
bella_companion/simulations/scenarios/__init__.py
bella_companion/simulations/scenarios/common.py
bella_companion/simulations/scenarios/epi_multitype.py
bella_companion/simulations/scenarios/epi_skyline.py
bella_companion/simulations/scenarios/fbd_2traits.py
bella_companion/simulations/scenarios/fbd_no_traits.py
bella_companion/simulations/scenarios/scenario.py
bella_companion/simulations/scenarios/__pycache__/__init__.cpython-310.pyc
bella_companion/simulations/scenarios/__pycache__/common.cpython-310.pyc
bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-310.pyc
bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-310.pyc
bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-310.pyc
bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-310.pyc
bella_companion/simulations/scenarios/__pycache__/scenario.cpython-310.pyc
bella_companion/utils/__init__.py
bella_companion/utils/beast.py
bella_companion/utils/explain.py
bella_companion/utils/slurm.py
bella_companion/utils/__pycache__/__init__.cpython-310.pyc
bella_companion/utils/__pycache__/beast.cpython-310.pyc
bella_companion/utils/__pycache__/explain.cpython-310.pyc
bella_companion/utils/__pycache__/slurm.cpython-310.pyc