.gitignore
.readthedocs.yml
LICENSE.txt
MANIFEST.in
README.md
environment.yml
mkdocs.yml
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.pyf
dadi/integration_shared.c
dadi/integration_shared.h
dadi/tridiag.c
dadi/tridiag.h
dadi/tridiag.pyf
dadi.egg-info/PKG-INFO
dadi.egg-info/SOURCES.txt
dadi.egg-info/dependency_links.txt
dadi.egg-info/requires.txt
dadi.egg-info/top_level.txt
dadi/DFE/Cache1D_mod.py
dadi/DFE/Cache2D_mod.py
dadi/DFE/DemogSelModels.py
dadi/DFE/LICENSE
dadi/DFE/PDFs.c
dadi/DFE/PDFs.py
dadi/DFE/PDFs.pyf
dadi/DFE/Plotting.py
dadi/DFE/__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.pyx
dadi/Triallele/transition12.pyx
dadi/Triallele/transition1D.pyx
dadi/Triallele/transition2.pyx
dadi/TwoLocus/TLSpectrum_mod.py
dadi/TwoLocus/__init__.py
dadi/TwoLocus/demographics.py
dadi/TwoLocus/inference.py
dadi/TwoLocus/integration.py
dadi/TwoLocus/numerics.py
dadi/TwoLocus/plotting.py
dadi/TwoLocus/projection_genotypes.pyx
dadi/TwoLocus/surface_interaction.pyx
dadi/TwoLocus/transition1.pyx
dadi/TwoLocus/transition12.pyx
dadi/TwoLocus/transition13.pyx
dadi/TwoLocus/transition1D.pyx
dadi/TwoLocus/transition2.pyx
dadi/TwoLocus/transition23.pyx
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
doc/api/dadi/Triallele/numerics.html
doc/api/dadi/Triallele/plotting.html
doc/api/dadi/TwoLocus/TLSpectrum_mod.html
doc/api/dadi/TwoLocus/demographics.html
doc/api/dadi/TwoLocus/index.html
doc/api/dadi/TwoLocus/inference.html
doc/api/dadi/TwoLocus/integration.html
doc/api/dadi/TwoLocus/numerics.html
doc/api/dadi/TwoLocus/plotting.html
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
doc/user-guide/plotting.md
doc/user-guide/polyploid-subgenomes.md
doc/user-guide/references.md
doc/user-guide/simulation-and-fitting.md
doc/user-guide/specifying-a-model.md
doc/user-guide/triallelic-spectra.md
doc/user-guide/uncertainty-analysis.md
examples/.DS_Store
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/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
examples/Triallele/tri.fs
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
examples/YRI_CEU/YRI_CEU.py
examples/YRI_CEU/demographic_models.py
examples/YRI_CEU/bootstraps/00.fs
examples/YRI_CEU/bootstraps/01.fs
examples/YRI_CEU/bootstraps/02.fs
examples/YRI_CEU/bootstraps/03.fs
examples/YRI_CEU/bootstraps/04.fs
examples/YRI_CEU/bootstraps/05.fs
examples/YRI_CEU/bootstraps/06.fs
examples/YRI_CEU/bootstraps/07.fs
examples/YRI_CEU/bootstraps/08.fs
examples/YRI_CEU/bootstraps/09.fs
examples/YRI_CEU/bootstraps/10.fs
examples/YRI_CEU/bootstraps/11.fs
examples/YRI_CEU/bootstraps/12.fs
examples/YRI_CEU/bootstraps/13.fs
examples/YRI_CEU/bootstraps/14.fs
examples/YRI_CEU/bootstraps/15.fs
examples/YRI_CEU/bootstraps/16.fs
examples/YRI_CEU/bootstraps/17.fs
examples/YRI_CEU/bootstraps/18.fs
examples/YRI_CEU/bootstraps/19.fs
examples/YRI_CEU/bootstraps/20.fs
examples/YRI_CEU/bootstraps/21.fs
examples/YRI_CEU/bootstraps/22.fs
examples/YRI_CEU/bootstraps/23.fs
examples/YRI_CEU/bootstraps/24.fs
examples/YRI_CEU/bootstraps/25.fs
examples/YRI_CEU/bootstraps/26.fs
examples/YRI_CEU/bootstraps/27.fs
examples/YRI_CEU/bootstraps/28.fs
examples/YRI_CEU/bootstraps/29.fs
examples/YRI_CEU/bootstraps/30.fs
examples/YRI_CEU/bootstraps/31.fs
examples/YRI_CEU/bootstraps/32.fs
examples/YRI_CEU/bootstraps/33.fs
examples/YRI_CEU/bootstraps/34.fs
examples/YRI_CEU/bootstraps/35.fs
examples/YRI_CEU/bootstraps/36.fs
examples/YRI_CEU/bootstraps/37.fs
examples/YRI_CEU/bootstraps/38.fs
examples/YRI_CEU/bootstraps/39.fs
examples/YRI_CEU/bootstraps/40.fs
examples/YRI_CEU/bootstraps/41.fs
examples/YRI_CEU/bootstraps/42.fs
examples/YRI_CEU/bootstraps/43.fs
examples/YRI_CEU/bootstraps/44.fs
examples/YRI_CEU/bootstraps/45.fs
examples/YRI_CEU/bootstraps/46.fs
examples/YRI_CEU/bootstraps/47.fs
examples/YRI_CEU/bootstraps/48.fs
examples/YRI_CEU/bootstraps/49.fs
examples/YRI_CEU/bootstraps/50.fs
examples/YRI_CEU/bootstraps/51.fs
examples/YRI_CEU/bootstraps/52.fs
examples/YRI_CEU/bootstraps/53.fs
examples/YRI_CEU/bootstraps/54.fs
examples/YRI_CEU/bootstraps/55.fs
examples/YRI_CEU/bootstraps/56.fs
examples/YRI_CEU/bootstraps/57.fs
examples/YRI_CEU/bootstraps/58.fs
examples/YRI_CEU/bootstraps/59.fs
examples/YRI_CEU/bootstraps/60.fs
examples/YRI_CEU/bootstraps/61.fs
examples/YRI_CEU/bootstraps/62.fs
examples/YRI_CEU/bootstraps/63.fs
examples/YRI_CEU/bootstraps/64.fs
examples/YRI_CEU/bootstraps/65.fs
examples/YRI_CEU/bootstraps/66.fs
examples/YRI_CEU/bootstraps/67.fs
examples/YRI_CEU/bootstraps/68.fs
examples/YRI_CEU/bootstraps/69.fs
examples/YRI_CEU/bootstraps/70.fs
examples/YRI_CEU/bootstraps/71.fs
examples/YRI_CEU/bootstraps/72.fs
examples/YRI_CEU/bootstraps/73.fs
examples/YRI_CEU/bootstraps/74.fs
examples/YRI_CEU/bootstraps/75.fs
examples/YRI_CEU/bootstraps/76.fs
examples/YRI_CEU/bootstraps/77.fs
examples/YRI_CEU/bootstraps/78.fs
examples/YRI_CEU/bootstraps/79.fs
examples/YRI_CEU/bootstraps/80.fs
examples/YRI_CEU/bootstraps/81.fs
examples/YRI_CEU/bootstraps/82.fs
examples/YRI_CEU/bootstraps/83.fs
examples/YRI_CEU/bootstraps/84.fs
examples/YRI_CEU/bootstraps/85.fs
examples/YRI_CEU/bootstraps/86.fs
examples/YRI_CEU/bootstraps/87.fs
examples/YRI_CEU/bootstraps/88.fs
examples/YRI_CEU/bootstraps/89.fs
examples/YRI_CEU/bootstraps/90.fs
examples/YRI_CEU/bootstraps/91.fs
examples/YRI_CEU/bootstraps/92.fs
examples/YRI_CEU/bootstraps/93.fs
examples/YRI_CEU/bootstraps/94.fs
examples/YRI_CEU/bootstraps/95.fs
examples/YRI_CEU/bootstraps/96.fs
examples/YRI_CEU/bootstraps/97.fs
examples/YRI_CEU/bootstraps/98.fs
examples/YRI_CEU/bootstraps/99.fs
examples/demes_test/phi.npy
examples/demes_test/test1.out
examples/demes_test/test2.out
examples/fs_from_data/.DS_Store
examples/fs_from_data/1KG.YRI.CEU.biallelic.synonymous.snps.withanc.strict.subset.vcf.gz
examples/fs_from_data/1KG.YRI.CEU.popfile.txt
examples/fs_from_data/ZI_Chr2R_1_1000000.fixed.vcf
examples/fs_from_data/ZI_Chr2R_1_1000000.vcf
examples/fs_from_data/ZI_Chr2R_4000000_5000000.fixed.vcf
examples/fs_from_data/ZI_Chr2R_4000000_5000000.vcf
examples/fs_from_data/fix_PopFly.py
examples/fs_from_data/fs_from_data.ipynb
examples/fs_from_data/fs_from_data.py
examples/fs_from_data/genetic_map_comeron2012_dm6_chr2R.txt
examples/fs_from_data/test_scikit_allel.py
examples/fs_from_data/two_locus_vcf.py
tests/IM.fs
tests/admixture_test_manual.py
tests/out.txt
tests/run_tests.py
tests/test_1D_Integration.py
tests/test_2D_frozen1.fs
tests/test_4D.py
tests/test_5D.py
tests/test_Admixture.py
tests/test_CUDA.py
tests/test_DFE.py
tests/test_Freezing.py
tests/test_Inbreeding.py
tests/test_Optimization.py
tests/test_PhiManip.py
tests/test_Projection.py
tests/test_Results.py
tests/test_Spectrum.py
tests/test_Subgenomes.py
tests/test_Tridiagonal.py
tests/test_fs_from_data.py
tests/test_phi1D.py
tests/test_data/fitdadi.IM_2D_point_pos_test.fs
tests/test_data/fitdadi.IM_no_ext_test.fs
tests/test_data/fitdadi.IM_point_pos_test.fs
tests/test_data/fitdadi.IM_test.fs