.gitignore
.pre-commit-config.yaml
.readthedocs.yml
CHANGELOG.rst
CODE_OF_CONDUCT.md
LICENSE
README.md
environment.yml
pyproject.toml
setup.cfg
setup.py
stdpopsim_example.ipynb
validation.py
.github/dependabot.yml
.github/mergify.yml
.github/ISSUE_TEMPLATE/bug-report-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/tests.yml
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/do_not_delete
docs/_static/tute-divergence.png
docs/_static/tute-sfs.png
docs/_static/tute-sweep.png
docs/_templates/do_not_delete
docs/parameter_tables/AnaPla/MallardBlackDuck_2L19.csv
docs/parameter_tables/AnoGam/GabonAg1000G_1A17.csv
docs/parameter_tables/AraTha/African2Epoch_1H18.csv
docs/parameter_tables/AraTha/African3Epoch_1H18.csv
docs/parameter_tables/AraTha/SouthMiddleAtlas_1D17.csv
docs/parameter_tables/BosTau/HolsteinFriesian_1M13.csv
docs/parameter_tables/DroMel/African3Epoch_1S16.csv
docs/parameter_tables/DroMel/OutOfAfrica_2L06.csv
docs/parameter_tables/HomSap/Africa_1B08.csv
docs/parameter_tables/HomSap/Africa_1T12.csv
docs/parameter_tables/HomSap/AmericanAdmixture_4B11.csv
docs/parameter_tables/HomSap/AncientEurasia_9K19.csv
docs/parameter_tables/HomSap/AncientEurope_4A21.csv
docs/parameter_tables/HomSap/AshkSub_7G19.csv
docs/parameter_tables/HomSap/OutOfAfricaArchaicAdmixture_5R19.csv
docs/parameter_tables/HomSap/OutOfAfricaExtendedNeandertalAdmixturePulse_3I21.csv
docs/parameter_tables/HomSap/OutOfAfrica_2T12.csv
docs/parameter_tables/HomSap/OutOfAfrica_3G09.csv
docs/parameter_tables/HomSap/OutOfAfrica_4J17.csv
docs/parameter_tables/HomSap/PapuansOutOfAfrica_10J19.csv
docs/parameter_tables/HomSap/Zigzag_1S14.csv
docs/parameter_tables/PanTro/BonoboGhost_4K19.csv
docs/parameter_tables/PapAnu/SinglePopSMCpp_1W22.csv
docs/parameter_tables/PonAbe/TwoSpecies_2L11.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
stdpopsim/__init__.py
stdpopsim/__main__.py
stdpopsim/_version.py
stdpopsim/annotations.py
stdpopsim/cache.py
stdpopsim/citations.py
stdpopsim/cli.py
stdpopsim/dfe.py
stdpopsim/engines.py
stdpopsim/genetic_maps.py
stdpopsim/genomes.py
stdpopsim/models.py
stdpopsim/slim_engine.py
stdpopsim/species.py
stdpopsim/utils.py
stdpopsim/warning_categories.py
stdpopsim.egg-info/PKG-INFO
stdpopsim.egg-info/SOURCES.txt
stdpopsim.egg-info/dependency_links.txt
stdpopsim.egg-info/entry_points.txt
stdpopsim.egg-info/not-zip-safe
stdpopsim.egg-info/requires.txt
stdpopsim.egg-info/top_level.txt
stdpopsim/catalog/__init__.py
stdpopsim/catalog/ensembl_info.py
stdpopsim/catalog/AedAeg/__init__.py
stdpopsim/catalog/AedAeg/genome_data.py
stdpopsim/catalog/AedAeg/species.py
stdpopsim/catalog/AnaPla/__init__.py
stdpopsim/catalog/AnaPla/demographic_models.py
stdpopsim/catalog/AnaPla/genome_data.py
stdpopsim/catalog/AnaPla/species.py
stdpopsim/catalog/AnoCar/__init__.py
stdpopsim/catalog/AnoCar/genome_data.py
stdpopsim/catalog/AnoCar/species.py
stdpopsim/catalog/AnoGam/__init__.py
stdpopsim/catalog/AnoGam/demographic_models.py
stdpopsim/catalog/AnoGam/genome_data.py
stdpopsim/catalog/AnoGam/species.py
stdpopsim/catalog/ApiMel/__init__.py
stdpopsim/catalog/ApiMel/genome_data.py
stdpopsim/catalog/ApiMel/species.py
stdpopsim/catalog/AraTha/__init__.py
stdpopsim/catalog/AraTha/annotations.py
stdpopsim/catalog/AraTha/demographic_models.py
stdpopsim/catalog/AraTha/dfes.py
stdpopsim/catalog/AraTha/genetic_maps.py
stdpopsim/catalog/AraTha/genome_data.py
stdpopsim/catalog/AraTha/species.py
stdpopsim/catalog/BosTau/__init__.py
stdpopsim/catalog/BosTau/demographic_models.py
stdpopsim/catalog/BosTau/genome_data.py
stdpopsim/catalog/BosTau/species.py
stdpopsim/catalog/CaeEle/__init__.py
stdpopsim/catalog/CaeEle/genetic_maps.py
stdpopsim/catalog/CaeEle/genome_data.py
stdpopsim/catalog/CaeEle/species.py
stdpopsim/catalog/CanFam/__init__.py
stdpopsim/catalog/CanFam/genetic_maps.py
stdpopsim/catalog/CanFam/genome_data.py
stdpopsim/catalog/CanFam/species.py
stdpopsim/catalog/ChlRei/__init__.py
stdpopsim/catalog/ChlRei/genome_data.py
stdpopsim/catalog/ChlRei/species.py
stdpopsim/catalog/DroMel/__init__.py
stdpopsim/catalog/DroMel/annotations.py
stdpopsim/catalog/DroMel/demographic_models.py
stdpopsim/catalog/DroMel/dfes.py
stdpopsim/catalog/DroMel/genetic_maps.py
stdpopsim/catalog/DroMel/genome_data.py
stdpopsim/catalog/DroMel/species.py
stdpopsim/catalog/DroSec/__init__.py
stdpopsim/catalog/DroSec/genome_data.py
stdpopsim/catalog/DroSec/species.py
stdpopsim/catalog/EscCol/__init__.py
stdpopsim/catalog/EscCol/genome_data.py
stdpopsim/catalog/EscCol/species.py
stdpopsim/catalog/GasAcu/__init__.py
stdpopsim/catalog/GasAcu/genome_data.py
stdpopsim/catalog/GasAcu/species.py
stdpopsim/catalog/HelAnn/__init__.py
stdpopsim/catalog/HelAnn/genome_data.py
stdpopsim/catalog/HelAnn/species.py
stdpopsim/catalog/HelMel/__init__.py
stdpopsim/catalog/HelMel/genome_data.py
stdpopsim/catalog/HelMel/species.py
stdpopsim/catalog/HomSap/__init__.py
stdpopsim/catalog/HomSap/annotations.py
stdpopsim/catalog/HomSap/demographic_models.py
stdpopsim/catalog/HomSap/dfes.py
stdpopsim/catalog/HomSap/genetic_maps.py
stdpopsim/catalog/HomSap/genome_data.py
stdpopsim/catalog/HomSap/species.py
stdpopsim/catalog/PanTro/__init__.py
stdpopsim/catalog/PanTro/demographic_models.py
stdpopsim/catalog/PanTro/genome_data.py
stdpopsim/catalog/PanTro/species.py
stdpopsim/catalog/PapAnu/__init__.py
stdpopsim/catalog/PapAnu/demographic_models.py
stdpopsim/catalog/PapAnu/genetic_maps.py
stdpopsim/catalog/PapAnu/genome_data.py
stdpopsim/catalog/PapAnu/species.py
stdpopsim/catalog/PonAbe/__init__.py
stdpopsim/catalog/PonAbe/demographic_models.py
stdpopsim/catalog/PonAbe/genetic_maps.py
stdpopsim/catalog/PonAbe/genome_data.py
stdpopsim/catalog/PonAbe/species.py
stdpopsim/catalog/StrAga/__init__.py
stdpopsim/catalog/StrAga/genome_data.py
stdpopsim/catalog/StrAga/species.py
stdpopsim/ext/__init__.py
stdpopsim/ext/selection.py
stdpopsim/qc/AnaPla.py
stdpopsim/qc/AnoGam.py
stdpopsim/qc/AraTha.py
stdpopsim/qc/BosTau.py
stdpopsim/qc/DroMel.py
stdpopsim/qc/HomSap.py
stdpopsim/qc/PanTro.py
stdpopsim/qc/PapAnu.py
stdpopsim/qc/PonAbe.py
stdpopsim/qc/__init__.py
tests/__init__.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_HelAnn.py
tests/test_HelMel.py
tests/test_HomSap.py
tests/test_PanTro.py
tests/test_PapAnu.py
tests/test_PonAbe.py
tests/test_StrAga.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_ensembl.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