LICENSE
MANIFEST.in
README.md
pyproject.toml
snpio/__init__.py
snpio/benchmark_json.py
snpio/run_snpio.py
snpio.egg-info/PKG-INFO
snpio.egg-info/SOURCES.txt
snpio.egg-info/dependency_links.txt
snpio.egg-info/entry_points.txt
snpio.egg-info/requires.txt
snpio.egg-info/top_level.txt
snpio/analysis/__init__.py
snpio/analysis/allele_summary_stats.py
snpio/analysis/genotype_encoder.py
snpio/analysis/tree_parser.py
snpio/docs/source/conf.py
snpio/example_data/phylip_files/__init__.py
snpio/example_data/popmaps/__init__.py
snpio/example_data/structure_files/__init__.py
snpio/example_data/trees/__init__.py
snpio/filtering/__init__.py
snpio/filtering/filtering_helper.py
snpio/filtering/filtering_methods.py
snpio/filtering/nremover2.py
snpio/img/snpio_logo.png
snpio/io/__init__.py
snpio/io/genepop_reader.py
snpio/io/phylip_reader.py
snpio/io/structure_reader.py
snpio/io/vcf_reader.py
snpio/plotting/__init__.py
snpio/plotting/linkage_disequilibrium.py
snpio/plotting/plotting.py
snpio/popgenstats/__init__.py
snpio/popgenstats/amova.py
snpio/popgenstats/d_statistics.py
snpio/popgenstats/dfoil.py
snpio/popgenstats/dstat.py
snpio/popgenstats/dstats_base.py
snpio/popgenstats/fst_distance.py
snpio/popgenstats/fst_outlier_results.py
snpio/popgenstats/fst_outliers.py
snpio/popgenstats/fst_outliers_dbscan.py
snpio/popgenstats/fst_outliers_perm.py
snpio/popgenstats/genetic_distance.py
snpio/popgenstats/ld_polynomials.py
snpio/popgenstats/linkage_disequilibrium.py
snpio/popgenstats/numba_helpers.py
snpio/popgenstats/partd.py
snpio/popgenstats/pop_gen_statistics.py
snpio/popgenstats/stats.py
snpio/popgenstats/summary_statistics.py
snpio/read_input/__init__.py
snpio/read_input/genotype_data.py
snpio/read_input/genotype_data_base.py
snpio/read_input/popmap_file.py
snpio/utils/__init__.py
snpio/utils/benchmarking.py
snpio/utils/containers.py
snpio/utils/custom_exceptions.py
snpio/utils/logging.py
snpio/utils/misc.py
snpio/utils/missing_stats.py
snpio/utils/multiqc_reporter.py
snpio/utils/numeric.py
snpio/utils/output_paths.py
snpio/utils/plot_queue.py
snpio/utils/results_exporter.py
snpio/utils/sequence_tools.py
snpio/validation/__init__.py
snpio/validation/ld_plots.py
snpio/validation/ld_simulation.py
snpio/validation/linkage_disequilibrium.py
snpio/validation/data/moments_popgen_1_6_0_golden.csv.gz
snpio/validation/data/moments_popgen_1_6_0_golden.json
tests/test_allele_summary_stats.py
tests/test_dfoil.py
tests/test_dstats.py
tests/test_fst_outliers.py
tests/test_genepop_reader.py
tests/test_genotype_encoder.py
tests/test_ld_validation.py
tests/test_linkage_disequilibrium.py
tests/test_multiqc_config.py
tests/test_multiqc_reporter.py
tests/test_nremover2.py
tests/test_output_paths.py
tests/test_phylip_reader.py
tests/test_plotting.py
tests/test_pop_gen_statistics.py
tests/test_run_snpio.py
tests/test_structure_reader.py
tests/test_vcf_reader.py
tests/test_verify_distributions.py