.gitignore
.readthedocs.yml
LICENSE.txt
MANIFEST.in
README.md
environment.yml
mkdocs.yml
pyproject.toml
setup.py
dadi/Demographics1D.py
dadi/Demographics2D.py
dadi/Godambe.py
dadi/Inference.py
dadi/Integration.py
dadi/Misc.py
dadi/NLopt_mod.py
dadi/Numerics.py
dadi/PhiManip.py
dadi/Plotting.py
dadi/Spectrum_mod.py
dadi/__init__.py
dadi/integration1D.c
dadi/integration2D.c
dadi/integration3D.c
dadi/integration4D.c
dadi/integration5D.c
dadi/integration_c.c
dadi/integration_c.pyf
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dadi/tridiag.c
dadi/tridiag.h
dadi/tridiag.pyf
dadi/tridiag_cython.c
dadi/tridiag_cython.pyx
dadi-distributed/.gitignore
dadi-distributed/dd-cli-workqueue.py
dadi-distributed/dd-local.py
dadi-distributed/dd-workqueue.py
dadi-distributed/example_sbatch.sh
dadi-distributed/infer_dm.py
dadi/DFE/Cache1D_mod.py
dadi/DFE/Cache2D_mod.py
dadi/DFE/DemogSelModels.py
dadi/DFE/LICENSE
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dadi/DFE/PDFs_cython.pyx
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dadi/Demes/Demes.py
dadi/Demes/__init__.py
dadi/Triallele/TriSpectrum_mod.py
dadi/Triallele/__init__.py
dadi/Triallele/demographics.py
dadi/Triallele/integration.py
dadi/Triallele/numerics.py
dadi/Triallele/plotting.py
dadi/Triallele/transition1.c
dadi/Triallele/transition1.pyx
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dadi/Triallele/transition12.pyx
dadi/Triallele/transition1D.c
dadi/Triallele/transition1D.pyx
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dadi/Triallele/transition2.pyx
dadi/TwoLocus/TLSpectrum_mod.py
dadi/TwoLocus/__init__.py
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dadi/TwoLocus/inference.py
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dadi/TwoLocus/projection_genotypes.c
dadi/TwoLocus/projection_genotypes.pyx
dadi/TwoLocus/surface_interaction.c
dadi/TwoLocus/surface_interaction.pyx
dadi/TwoLocus/transition1.c
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dadi/TwoLocus/transition12.c
dadi/TwoLocus/transition12.pyx
dadi/TwoLocus/transition13.c
dadi/TwoLocus/transition13.pyx
dadi/TwoLocus/transition1D.c
dadi/TwoLocus/transition1D.pyx
dadi/TwoLocus/transition2.c
dadi/TwoLocus/transition2.pyx
dadi/TwoLocus/transition23.c
dadi/TwoLocus/transition23.pyx
dadi/TwoLocus/transition3.c
dadi/TwoLocus/transition3.pyx
dadi/cuda/Integration.py
dadi/cuda/__init__.py
dadi/cuda/cusparse.py
dadi/cuda/kernels.cu
dadi/cuda/kernels.py
doc/index.md
doc/requirements.txt
doc/api/dadi/Demographics1D.html
doc/api/dadi/Demographics2D.html
doc/api/dadi/Godambe.html
doc/api/dadi/Inference.html
doc/api/dadi/Integration.html
doc/api/dadi/Misc.html
doc/api/dadi/NLopt_mod.html
doc/api/dadi/Numerics.html
doc/api/dadi/PhiManip.html
doc/api/dadi/Plotting.html
doc/api/dadi/Spectrum_mod.html
doc/api/dadi/index.html
doc/api/dadi/DFE/Cache1D_mod.html
doc/api/dadi/DFE/Cache2D_mod.html
doc/api/dadi/DFE/DemogSelModels.html
doc/api/dadi/DFE/PDFs.html
doc/api/dadi/DFE/Plotting.html
doc/api/dadi/DFE/index.html
doc/api/dadi/Triallele/TriSpectrum_mod.html
doc/api/dadi/Triallele/demographics.html
doc/api/dadi/Triallele/index.html
doc/api/dadi/Triallele/integration.html
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doc/api/dadi/Triallele/plotting.html
doc/api/dadi/TwoLocus/TLSpectrum_mod.html
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doc/api/dadi/TwoLocus/numerics.html
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doc/examples/DFE/DFE.md
doc/examples/Triallele/TrialleleModel.md
doc/examples/TwoLocus/TwoLocusModel.md
doc/examples/YRI_CEU/YRI_CEU.md
doc/examples/fs_from_data/fs_from_data.md
doc/user-guide/GPU-computing.md
doc/user-guide/bootstrapping.md
doc/user-guide/dfe-inference.md
doc/user-guide/frequently-asked-questions.md
doc/user-guide/importing-data.md
doc/user-guide/inbreeding.md
doc/user-guide/installation.md
doc/user-guide/likelihood-ratio-test.md
doc/user-guide/manipulating-spectra.md
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doc/user-guide/simulation-and-fitting.md
doc/user-guide/specifying-a-model.md
doc/user-guide/triallelic-spectra.md
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examples/.DS_Store
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examples/pyproject_hatch.toml
examples/pyproject_ryan.toml
examples/CUDA/benchmark.py
examples/CUDA/models.py
examples/CUDA/models_moments.py
examples/CUDA/moments_comparison.py
examples/DFE/DFE.ipynb
examples/DFE/example.fs
examples/DFE/example1D.py
examples/DFE/example2D.py
examples/DFE copy/Cache1D_mod.py
examples/DFE copy/Cache2D_mod.py
examples/DFE copy/DemogSelModels.py
examples/DFE copy/LICENSE
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examples/Triallele/Triallele.ipynb
examples/Triallele/example_triallele_model.py
examples/Triallele/intervals_nu2.0_tau.1_ns20.txt
examples/Triallele/jenkins_comp.py
examples/Triallele/tree_script.r
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examples/TwoLocus/TwoLocus.ipynb
examples/TwoLocus/example.py
examples/TwoLocus/example_observed_fs.fs
examples/TwoLocus/two_epoch_example.fs
examples/YRI_CEU/YRI_CEU.fs
examples/YRI_CEU/YRI_CEU.ipynb
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