.gitignore
.pre-commit-config.yaml
.readthedocs.yml
CHANGELOG.rst
CODE_OF_CONDUCT.md
LICENSE
README.md
environment.yml
pyproject.toml
setup.cfg
setup.py
stdgrimmsim_example.ipynb
validation.py
.github/dependabot.yml
.github/mergify.yml
.github/ISSUE_TEMPLATE/bug-report-issue-template.md
.github/ISSUE_TEMPLATE/dfe-qc-issue-template.md
.github/ISSUE_TEMPLATE/feature-request-issue-template.md
.github/ISSUE_TEMPLATE/model-qc-issue-template.md
.github/ISSUE_TEMPLATE/new-species-issue-template.md
.github/ISSUE_TEMPLATE/species-qc-issue-template.md
.github/workflows/docs.yml
.github/workflows/pre-commit.yml
.github/workflows/publish-pypi.yml
.github/workflows/tests.yml
.test/README.txt
.test/install_and_run.sh
.test/run_cli_test.sh
.test/run_simulation.py
.test/run_slim_test.py
docs/Makefile
docs/api.rst
docs/catalog.rst
docs/changelogs.rst
docs/cli_arguments.rst
docs/conf.py
docs/development.rst
docs/docutils.conf
docs/examples.py
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/selection_example.py
docs/tutorial.rst
docs/_ext/speciescatalog.py
docs/_static/custom.css
docs/_static/do_not_delete
docs/_static/logo.png
docs/_static/tute-divergence.png
docs/_static/tute-sfs.png
docs/_static/tute-sweep.png
docs/_templates/do_not_delete
docs/_templates/footer.html
docs/parameter_tables/CthGre/DeepSlumber_1R28.csv
docs/parameter_tables/CthGre/RlyehRising_2P20.csv
docs/parameter_tables/DagHyd/HybridIntrogression_2M27.csv
docs/parameter_tables/DagHyd/InnsmouthDecline_1M27.csv
maintenance/__init__.py
maintenance/__main__.py
maintenance/annotation_maint.py
maintenance/ensembl.py
maintenance/liftOver.py
maintenance/liftOver_catalog.py
maintenance/liftOver_comeron2012.py
maintenance/main.py
maintenance/ncbi.py
requirements/development.txt
requirements/rtd-conda-environment.yml
requirements/CI/conda.txt
requirements/CI/requirements.txt
stdgrimmsim/__init__.py
stdgrimmsim/__main__.py
stdgrimmsim/_version.py
stdgrimmsim/annotations.py
stdgrimmsim/cache.py
stdgrimmsim/citations.py
stdgrimmsim/cli.py
stdgrimmsim/dfe.py
stdgrimmsim/engines.py
stdgrimmsim/genetic_maps.py
stdgrimmsim/genomes.py
stdgrimmsim/models.py
stdgrimmsim/selection.py
stdgrimmsim/slim_engine.py
stdgrimmsim/species.py
stdgrimmsim/utils.py
stdgrimmsim/warning_categories.py
stdgrimmsim.egg-info/PKG-INFO
stdgrimmsim.egg-info/SOURCES.txt
stdgrimmsim.egg-info/dependency_links.txt
stdgrimmsim.egg-info/entry_points.txt
stdgrimmsim.egg-info/not-zip-safe
stdgrimmsim.egg-info/requires.txt
stdgrimmsim.egg-info/top_level.txt
stdgrimmsim/catalog/__init__.py
stdgrimmsim/catalog/AlpNac/__init__.py
stdgrimmsim/catalog/AlpNac/demographic_models.py
stdgrimmsim/catalog/AlpNac/genome_data.py
stdgrimmsim/catalog/AlpNac/species.py
stdgrimmsim/catalog/AscPut/__init__.py
stdgrimmsim/catalog/AscPut/demographic_models.py
stdgrimmsim/catalog/AscPut/genome_data.py
stdgrimmsim/catalog/AscPut/species.py
stdgrimmsim/catalog/BasRex/__init__.py
stdgrimmsim/catalog/BasRex/demographic_models.py
stdgrimmsim/catalog/BasRex/genome_data.py
stdgrimmsim/catalog/BasRex/species.py
stdgrimmsim/catalog/BerAlp/__init__.py
stdgrimmsim/catalog/BerAlp/demographic_models.py
stdgrimmsim/catalog/BerAlp/genome_data.py
stdgrimmsim/catalog/BerAlp/species.py
stdgrimmsim/catalog/BreSta/__init__.py
stdgrimmsim/catalog/BreSta/demographic_models.py
stdgrimmsim/catalog/BreSta/genome_data.py
stdgrimmsim/catalog/BreSta/species.py
stdgrimmsim/catalog/DraFeu/__init__.py
stdgrimmsim/catalog/DraFeu/demographic_models.py
stdgrimmsim/catalog/DraFeu/genome_data.py
stdgrimmsim/catalog/DraFeu/species.py
stdgrimmsim/catalog/ErlKoe/__init__.py
stdgrimmsim/catalog/ErlKoe/demographic_models.py
stdgrimmsim/catalog/ErlKoe/genome_data.py
stdgrimmsim/catalog/ErlKoe/species.py
stdgrimmsim/catalog/FeeFlu/__init__.py
stdgrimmsim/catalog/FeeFlu/demographic_models.py
stdgrimmsim/catalog/FeeFlu/genome_data.py
stdgrimmsim/catalog/FeeFlu/species.py
stdgrimmsim/catalog/FraHol/__init__.py
stdgrimmsim/catalog/FraHol/demographic_models.py
stdgrimmsim/catalog/FraHol/genome_data.py
stdgrimmsim/catalog/FraHol/species.py
stdgrimmsim/catalog/HeiCol/__init__.py
stdgrimmsim/catalog/HeiCol/demographic_models.py
stdgrimmsim/catalog/HeiCol/genome_data.py
stdgrimmsim/catalog/HeiCol/species.py
stdgrimmsim/catalog/HexWal/__init__.py
stdgrimmsim/catalog/HexWal/demographic_models.py
stdgrimmsim/catalog/HexWal/genome_data.py
stdgrimmsim/catalog/HexWal/species.py
stdgrimmsim/catalog/JotRie/__init__.py
stdgrimmsim/catalog/JotRie/demographic_models.py
stdgrimmsim/catalog/JotRie/genome_data.py
stdgrimmsim/catalog/JotRie/species.py
stdgrimmsim/catalog/KobHau/__init__.py
stdgrimmsim/catalog/KobHau/demographic_models.py
stdgrimmsim/catalog/KobHau/genome_data.py
stdgrimmsim/catalog/KobHau/species.py
stdgrimmsim/catalog/LinDra/__init__.py
stdgrimmsim/catalog/LinDra/demographic_models.py
stdgrimmsim/catalog/LinDra/genome_data.py
stdgrimmsim/catalog/LinDra/species.py
stdgrimmsim/catalog/LorRhe/__init__.py
stdgrimmsim/catalog/LorRhe/demographic_models.py
stdgrimmsim/catalog/LorRhe/genome_data.py
stdgrimmsim/catalog/LorRhe/species.py
stdgrimmsim/catalog/MasLak/__init__.py
stdgrimmsim/catalog/MasLak/demographic_models.py
stdgrimmsim/catalog/MasLak/genome_data.py
stdgrimmsim/catalog/MasLak/species.py
stdgrimmsim/catalog/MooBay/__init__.py
stdgrimmsim/catalog/MooBay/demographic_models.py
stdgrimmsim/catalog/MooBay/genome_data.py
stdgrimmsim/catalog/MooBay/species.py
stdgrimmsim/catalog/MueGei/__init__.py
stdgrimmsim/catalog/MueGei/demographic_models.py
stdgrimmsim/catalog/MueGei/genome_data.py
stdgrimmsim/catalog/MueGei/species.py
stdgrimmsim/catalog/NixRhe/__init__.py
stdgrimmsim/catalog/NixRhe/demographic_models.py
stdgrimmsim/catalog/NixRhe/genome_data.py
stdgrimmsim/catalog/NixRhe/species.py
stdgrimmsim/catalog/OstBal/__init__.py
stdgrimmsim/catalog/OstBal/demographic_models.py
stdgrimmsim/catalog/OstBal/genome_data.py
stdgrimmsim/catalog/OstBal/species.py
stdgrimmsim/catalog/PomBal/__init__.py
stdgrimmsim/catalog/PomBal/demographic_models.py
stdgrimmsim/catalog/PomBal/genome_data.py
stdgrimmsim/catalog/PomBal/species.py
stdgrimmsim/catalog/PukPru/__init__.py
stdgrimmsim/catalog/PukPru/demographic_models.py
stdgrimmsim/catalog/PukPru/genome_data.py
stdgrimmsim/catalog/PukPru/species.py
stdgrimmsim/catalog/RueHar/__init__.py
stdgrimmsim/catalog/RueHar/demographic_models.py
stdgrimmsim/catalog/RueHar/genome_data.py
stdgrimmsim/catalog/RueHar/species.py
stdgrimmsim/catalog/RumSti/__init__.py
stdgrimmsim/catalog/RumSti/demographic_models.py
stdgrimmsim/catalog/RumSti/genome_data.py
stdgrimmsim/catalog/RumSti/species.py
stdgrimmsim/catalog/SaxErz/__init__.py
stdgrimmsim/catalog/SaxErz/demographic_models.py
stdgrimmsim/catalog/SaxErz/genome_data.py
stdgrimmsim/catalog/SaxErz/species.py
stdgrimmsim/catalog/SchWar/__init__.py
stdgrimmsim/catalog/SchWar/demographic_models.py
stdgrimmsim/catalog/SchWar/genome_data.py
stdgrimmsim/catalog/SchWar/species.py
stdgrimmsim/catalog/SieRab/__init__.py
stdgrimmsim/catalog/SieRab/demographic_models.py
stdgrimmsim/catalog/SieRab/genome_data.py
stdgrimmsim/catalog/SieRab/species.py
stdgrimmsim/catalog/ValKri/__init__.py
stdgrimmsim/catalog/ValKri/demographic_models.py
stdgrimmsim/catalog/ValKri/genome_data.py
stdgrimmsim/catalog/ValKri/species.py
stdgrimmsim/catalog/WerWol/__init__.py
stdgrimmsim/catalog/WerWol/demographic_models.py
stdgrimmsim/catalog/WerWol/genome_data.py
stdgrimmsim/catalog/WerWol/species.py
stdgrimmsim/catalog/WilJae/__init__.py
stdgrimmsim/catalog/WilJae/demographic_models.py
stdgrimmsim/catalog/WilJae/genome_data.py
stdgrimmsim/catalog/WilJae/species.py
stdgrimmsim/catalog/WolBay/__init__.py
stdgrimmsim/catalog/WolBay/demographic_models.py
stdgrimmsim/catalog/WolBay/genome_data.py
stdgrimmsim/catalog/WolBay/species.py
stdgrimmsim/catalog/ZweBerg/__init__.py
stdgrimmsim/catalog/ZweBerg/demographic_models.py
stdgrimmsim/catalog/ZweBerg/genome_data.py
stdgrimmsim/catalog/ZweBerg/species.py
stdgrimmsim/qc/__init__.py
tests/__init__.py
tests/conftest.py
tests/test_AedAeg.py
tests/test_AnaPla.py
tests/test_AnoCar.py
tests/test_AnoGam.py
tests/test_ApiMel.py
tests/test_AraTha.py
tests/test_BosTau.py
tests/test_CaeEle.py
tests/test_CanFam.py
tests/test_ChlRei.py
tests/test_DroMel.py
tests/test_DroSec.py
tests/test_EscCol.py
tests/test_GasAcu.py
tests/test_GorGor.py
tests/test_HelAnn.py
tests/test_HelMel.py
tests/test_HomSap.py
tests/test_MusMus.py
tests/test_OrySat.py
tests/test_PanTro.py
tests/test_PapAnu.py
tests/test_PhoSin.py
tests/test_PonAbe.py
tests/test_RatNor.py
tests/test_StrAga.py
tests/test_SusScr.py
tests/test_annotations.py
tests/test_cache.py
tests/test_citations.py
tests/test_cli.py
tests/test_dfes.py
tests/test_engines.py
tests/test_genetic_maps.py
tests/test_genomes.py
tests/test_maintenance.py
tests/test_masking.py
tests/test_models.py
tests/test_slim_engine.py
tests/test_species.py
tests/test_utils.py