.gitignore
LICENSE.txt
MANIFEST.in
README.md
epydoc.config
pyproject.toml
requirements.txt
setup.py
.github/workflows/build_docs.yml
.github/workflows/tests.yml
.github/workflows/wheels.yml
bench/bench.py
bench/demographic_models_dadi.py
bench/demographic_models_moments.py
bench/gen_lim_fs_extrap.py
bench/report.py
docs/Makefile
docs/conf.py
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/make.bat
docs/_static/README
docs/api/api_demes.rst
docs/api/api_ld.rst
docs/api/api_moments.rst
docs/data/bootstrap_sets.split_mig.100_reps.bp
docs/data/h30rho.gz
docs/data/im-parsing-example.ld_stats.bp
docs/data/im-parsing-example.map.txt
docs/data/im-parsing-example.samples.pops.txt
docs/data/im-parsing-example.vcf
docs/data/im-parsing-example.yaml
docs/data/means.varcovs.split_mig.100_reps.bp
docs/data/msl_best_fit_model.yaml
docs/data/msl_data.bp
docs/data/msl_initial_model.yaml
docs/data/msl_options.yaml
docs/data/msl_spectrum_cache.bp
docs/data/msl_spectrum_cache_two_epoch.bp
docs/data/ooa.10.10.10.fs
docs/data/ooa.ceu_ancient.10.10.fs
docs/data/ooa.yri.40.fs
docs/data/ooa.yri.40.sel.fs
docs/data/plot_msl_spectra.py
docs/data/two-deme-example-best-fit.yaml
docs/data/two-deme-example-data.bp
docs/data/two-deme-example-options.yaml
docs/data/two-deme-example.yaml
docs/data/two-locus/eq.n_30.rho_0.5.fs.gz
docs/data/two-locus/eq.n_30.rho_0.5.sel_-1.0_-1_-1.fs.gz
docs/data/two-locus/eq.n_30.rho_0.5.sel_-20.0_-20_-20.fs.gz
docs/data/two-locus/eq.n_30.rho_0.5.sel_-2_-1_-1.fs.gz
docs/data/two-locus/eq.n_30.rho_0.5.sel_-40_-20_-20.fs.gz
docs/data/two-locus/eq.n_30.rho_0.5.sel_-4_-1_-1.fs.gz
docs/data/two-locus/eq.n_30.rho_0.5.sel_-80_-20_-20.fs.gz
docs/data/two-locus/eq.n_30.rho_30.0.fs.gz
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docs/data/two-locus/eq.n_30.rho_5.0.sel_-80_-20_-20.fs.gz
docs/extensions/demes.rst
docs/extensions/triallele.rst
docs/extensions/two_locus.rst
docs/figures/ancestral_misid.png
docs/figures/msl_lof_comparison.png
docs/figures/msl_mis_comparison.png
docs/figures/msl_spectra.png
docs/figures/msl_syn_comparison.png
docs/ld/inference.rst
docs/ld/ld.rst
docs/ld/parsing.rst
docs/modules/dfe.rst
docs/modules/diversity.rst
docs/modules/recombination.rst
docs/modules/two_locus_selection.rst
docs/sfs/inference.rst
docs/sfs/parsing.rst
docs/sfs/sfs.rst
examples/variable_migration.py
examples/LD/OOA.py
examples/LD/parsing-and-inference-example.py
examples/YRI_CEU/YRI_CEU.fs
examples/YRI_CEU/YRI_CEU.py
examples/YRI_CEU/demographic_models.py
examples/demes_inference/data.uL_0.36.fs
examples/demes_inference/gutenkunst_ooa.yml
examples/demes_inference/inference_options.yml
examples/demes_inference/run_optimization.py
examples/fs_from_angsd/demog_infer_moments.py
examples/fs_from_angsd/parse_angsd_output.py
examples/fs_from_data/Q.HwangGreen.human.dat
examples/fs_from_data/data.txt
examples/fs_from_data/fs_from_data.py
examples/fs_from_data/fux_table.dat
examples/fs_from_data/tri_freq.dat
examples/parsing_ld_from_multiple_chromosomes/multichrom.bed
examples/parsing_ld_from_multiple_chromosomes/multichrom_parsing_example.py
examples/sfs_inference_time_series/model.yaml
examples/sfs_inference_time_series/options.yaml
examples/sfs_inference_time_series/simulate_data.py
moments/Demographics1D.py
moments/Demographics2D.py
moments/Demographics3D.py
moments/Godambe.py
moments/Inference.py
moments/Integration.py
moments/Integration_nomig.py
moments/Jackknife.c
moments/Jackknife.pyx
moments/LinearSystem.py
moments/LinearSystem_1D.c
moments/LinearSystem_1D.pyx
moments/LinearSystem_2D.c
moments/LinearSystem_2D.pyx
moments/Manips.py
moments/Misc.py
moments/ModelPlot.py
moments/Numerics.py
moments/Parsing.py
moments/Plotting.py
moments/Reversible.py
moments/Spectrum_mod.py
moments/Tridiag_solve.c
moments/Tridiag_solve.pyx
moments/__init__.py
moments/_version.py
moments/Demes/Demes.py
moments/Demes/DemesUtil.py
moments/Demes/Inference.py
moments/Demes/__init__.py
moments/LD/Demographics1D.py
moments/LD/Demographics2D.py
moments/LD/Demographics3D.py
moments/LD/Godambe.py
moments/LD/Inference.py
moments/LD/LDstats_mod.py
moments/LD/Matrices.py
moments/LD/Numerics.py
moments/LD/Parsing.py
moments/LD/Plotting.py
moments/LD/Util.py
moments/LD/__init__.py
moments/LD/genotype_calculations.c
moments/LD/genotype_calculations.pyx
moments/LD/genotype_calculations_multipop.c
moments/LD/genotype_calculations_multipop.pyx
moments/LD/sparse_tallying.c
moments/LD/sparse_tallying.pyx
moments/LD/stats_from_genotype_counts.py
moments/LD/stats_from_haplotype_counts.py
moments/Triallele/Demographics.py
moments/Triallele/Integration.py
moments/Triallele/Jackknife.py
moments/Triallele/Numerics.py
moments/Triallele/TriSpectrum_mod.py
moments/Triallele/__init__.py
moments/TwoLocus/Demographics.py
moments/TwoLocus/Inference.py
moments/TwoLocus/Integration.py
moments/TwoLocus/Jackknife.py
moments/TwoLocus/Numerics.py
moments/TwoLocus/TLSpectrum_mod.py
moments/TwoLocus/Util.py
moments/TwoLocus/__init__.py
moments_popgen.egg-info/PKG-INFO
moments_popgen.egg-info/SOURCES.txt
moments_popgen.egg-info/dependency_links.txt
moments_popgen.egg-info/requires.txt
moments_popgen.egg-info/top_level.txt
requirements/lint.txt
requirements/tests.txt
tests/readme.md
tests/run_tests.py
tests/test_Demes.py
tests/test_DemesTimeWindows.py
tests/test_DistanceConstrained.py
tests/test_Fstatistics.py
tests/test_GenotypeCalculations.py
tests/test_Jackknife.py
tests/test_LD.py
tests/test_LDParsing.py
tests/test_LinearSystem.py
tests/test_Manips.py
tests/test_Migration.py
tests/test_Projection.py
tests/test_Results.py
tests/test_Reversible.py
tests/test_SFSParsing.py
tests/test_Selection.py
tests/test_Spectrum.py
tests/test_Triallele.py
tests/test_TwoLocus.py
tests/test_files/1_pop.fs
tests/test_files/2_pops.fs
tests/test_files/2_pops_neutral.fs
tests/test_files/3_pop_pop_file.txt
tests/test_files/3_pops.fs
tests/test_files/IM.fs
tests/test_files/basic_3_sample.vcf
tests/test_files/bed_file_full.bed
tests/test_files/bed_file_sparse.bed
tests/test_files/drift_matrix.csv
tests/test_files/drift_matrix_1D.csv
tests/test_files/fasta_file_full.fa
tests/test_files/fasta_file_large.fa
tests/test_files/fasta_file_low_conf.fa
tests/test_files/fasta_file_missing_data.fa
tests/test_files/format_DP_GQ_4_sample.vcf
tests/test_files/gutenkunst_ooa.yaml
tests/test_files/info_DP_GQ_3_sample.vcf
tests/test_files/invalid_pop_file.txt
tests/test_files/migration_matrix.csv
tests/test_files/missing_data_2_sample.vcf
tests/test_files/missing_data_3_sample.vcf
tests/test_files/multiallelic_2_sample.vcf
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tests/test_files/selection_matrix_1.csv
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