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CHANGELOG.rst
LICENSE
README.html
README.md
setup.py
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docs/.gitignore
docs/Makefile
docs/_config.yml
docs/_toc.yml
docs/annotate_genome.pdf
docs/annotated_p_vs_s.pdf
docs/build.sh
docs/conf.py
docs/development.md
docs/example_sim.slim
docs/installation.md
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docs/neutral_restart.slim
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docs/rapid_adaptation.slim
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docs/selection.slim
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docs/util.py
docs/vignette_coalescent_diversity.md
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docs/vignette_space.md
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pyslim/__init__.py
pyslim/_version.py
pyslim/methods.py
pyslim/provenance.py
pyslim/slim_metadata.py
pyslim/slim_tree_sequence.py
pyslim/spatial.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/CI-conda/requirements.txt
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tests/README.md
tests/__init__.py
tests/conftest.py
tests/recipe_specs.py
tests/test_annotation.py
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tests/extra_recipes/.gitignore
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tests/extra_recipes/Recipe 17.1 - A minimal tree-seq model.txt
tests/extra_recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt
tests/extra_recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation II.py
tests/extra_recipes/Recipe 17.2 - Overlaying neutral mutations.py
tests/extra_recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt
tests/extra_recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt
tests/extra_recipes/Recipe 17.4 - Detecting the dip in diversity (analyzing tree heights in Python) I.txt
tests/extra_recipes/Recipe 17.4 - Detecting the dip in diversity (analyzing tree heights in Python) II.py
tests/extra_recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt
tests/extra_recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) II.py
tests/extra_recipes/Recipe 17.7 - Analyzing selection coefficients in Python with tskit I.txt
tests/extra_recipes/Recipe 17.7 - Analyzing selection coefficients in Python with tskit II.py
tests/extra_recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history I.py
tests/extra_recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt
tests/extra_recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history III.py
tests/extra_recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history I.py
tests/extra_recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history II.txt
tests/extra_recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models I.txt
tests/extra_recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models II.py
tests/extra_recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models III.py
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