.codecov.yml
.gitignore
CHANGELOG.rst
LICENSE
README.html
README.md
setup.py
.circleci/config.yml
docs/.gitignore
docs/Makefile
docs/conf.py
docs/development.rst
docs/example_sim.slim
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/metadata.rst
docs/migrants.slim
docs/python_api.rst
docs/rapid_adaptation.slim
docs/selection.slim
docs/tutorial.rst
docs/vignette_continuing.rst
docs/vignette_space.rst
docs/vignette_space.slim
docs/_static/Makefile
docs/_static/export-layers-svg.sh
docs/_static/pedigree0.pdf
docs/_static/pedigree0.png
docs/_static/pedigree01.png
docs/_static/pedigree1.pdf
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docs/_static/pedigree2.pdf
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docs/_static/pedigree3.pdf
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docs/_static/pedigree_mutate.pdf
docs/_static/pedigree_mutate.png
docs/_static/pedigree_recapitate.pdf
docs/_static/pedigree_recapitate.png
docs/_static/pedigree_simplify.pdf
docs/_static/pedigree_simplify.png
docs/_static/pedigrees.ink.svg
docs/_static/recomb_rates.tsv
docs/_static/spatial_sim_ibd.png
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pyslim/__init__.py
pyslim/_version.py
pyslim/provenance.py
pyslim/slim_metadata.py
pyslim/slim_tree_sequence.py
pyslim/util.py
pyslim.egg-info/PKG-INFO
pyslim.egg-info/SOURCES.txt
pyslim.egg-info/dependency_links.txt
pyslim.egg-info/not-zip-safe
pyslim.egg-info/requires.txt
pyslim.egg-info/top_level.txt
requirements/conda-minimal.txt
requirements/rtd.txt
requirements/CI/requirements.txt
tests/__init__.py
tests/conftest.py
tests/test_annotation.py
tests/test_legacy_metadata.py
tests/test_metadata.py
tests/test_provenance.py
tests/test_tree_sequence.py
tests/test_util.py
tests/benchmark/annotation.sh
tests/benchmark/metadata.sh
tests/benchmark/metadata.slim
tests/examples/make_v3_tests.sh
tests/examples/recipe_WF.slim
tests/examples/recipe_WF.v3.0.trees
tests/examples/recipe_WF.v3.2.trees
tests/examples/recipe_WF.v3.3.1.trees
tests/examples/recipe_WF.v3.4.trees
tests/examples/recipe_WF_early.slim
tests/examples/recipe_WF_migration.slim
tests/examples/recipe_init_mutated_WF.slim
tests/examples/recipe_init_mutated_nonWF.slim
tests/examples/recipe_long_WF.slim
tests/examples/recipe_long_nonWF.slim
tests/examples/recipe_long_nucleotides.slim
tests/examples/recipe_nonWF.slim
tests/examples/recipe_nonWF.v3.0.trees
tests/examples/recipe_nonWF.v3.2.trees
tests/examples/recipe_nonWF.v3.3.1.trees
tests/examples/recipe_nonWF.v3.4.trees
tests/examples/recipe_nonWF_early.slim
tests/examples/recipe_nonWF_selfing.slim
tests/examples/recipe_nucleotides.slim
tests/examples/recipe_record_everyone_WF_early.slim
tests/examples/recipe_record_everyone_WF_late.slim
tests/examples/recipe_record_everyone_nonWF_early.slim
tests/examples/recipe_record_everyone_nonWF_late.slim
tests/examples/recipe_roots.slim
tests/examples/restart_WF.slim
tests/examples/restart_msprime.slim
tests/examples/restart_nonWF.slim
tests/examples/restart_nucleotides.slim
tests/recipes/.gitignore
tests/recipes/Makefile
tests/recipes/Recipe 17.1 - A minimal tree-seq model.txt
tests/recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt
tests/recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation II.py
tests/recipes/Recipe 17.2 - Overlaying neutral mutations.py
tests/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt
tests/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt
tests/recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt
tests/recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) II.py
tests/recipes/Recipe 17.7 - Analyzing selection coefficients in Python with pyslim I.txt
tests/recipes/Recipe 17.7 - Analyzing selection coefficients in Python with pyslim II.py
tests/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history I.py
tests/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt
tests/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history III.py
tests/recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history I.py
tests/recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history II.txt
tests/recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models I.txt
tests/recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models II.py
tests/recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models III.py
tests/recipes/check_trees.py