LICENSE
MANIFEST.in
README.md
pyproject.toml
snpio/__init__.py
snpio/benchmark_json.py
snpio/run_snpio.py
snpio/analysis/__init__.py
snpio/analysis/genotype_encoder.py
snpio/analysis/tree_parser.py
snpio/docs/HEADER.yaml
snpio/docs/Makefile
snpio/docs/admonitions-filter.lua
snpio/docs/admonitions.tex
snpio/docs/listings-setup.tex
snpio/docs/make.bat
snpio/docs/metadata.yaml
snpio/docs/requirements.txt
snpio/docs/template.tex
snpio/docs/dev/versioning.md
snpio/docs/source/changelog.md
snpio/docs/source/changelog.rst
snpio/docs/source/conf.py
snpio/docs/source/example_script.rst
snpio/docs/source/getting_started.rst
snpio/docs/source/index.rst
snpio/docs/source/modules.rst
snpio/docs/source/refs.bib
snpio/docs/source/snpio.analysis.rst
snpio/docs/source/snpio.filtering.rst
snpio/docs/source/snpio.io.rst
snpio/docs/source/snpio.plotting.rst
snpio/docs/source/snpio.popgenstats.rst
snpio/docs/source/snpio.read_input.rst
snpio/docs/source/snpio.rst
snpio/docs/source/snpio.utils.rst
snpio/docs/source/_static/custom.css
snpio/example_data/phylip_files/__init__.py
snpio/example_data/phylip_files/phylogen_nomx.u.snps.phy
snpio/example_data/popmaps/__init__.py
snpio/example_data/popmaps/phylogen_gusep.popmap
snpio/example_data/popmaps/phylogen_nomx.popmap
snpio/example_data/structure_files/__init__.py
snpio/example_data/structure_files/phylogen_nomx.ustr
snpio/example_data/structure_files/test.nopops.1row.10sites.str
snpio/example_data/structure_files/test.nopops.2row.100sites.str
snpio/example_data/structure_files/test.nopops.2row.10sites.str
snpio/example_data/structure_files/test.nopops.2row.30sites.str
snpio/example_data/structure_files/test.nopops.2row.allsites.str
snpio/example_data/structure_files/test.pops.1row.10sites.str
snpio/example_data/structure_files/test.pops.2row.10sites.str
snpio/example_data/structure_files/test.pops.2row.allsites.str
snpio/example_data/trees/__init__.py
snpio/example_data/trees/copy_rates.sh
snpio/example_data/trees/test.iqtree
snpio/example_data/trees/test.qmat
snpio/example_data/trees/test.rate
snpio/example_data/trees/test.tre
snpio/example_data/trees/test14K.rate
snpio/example_data/trees/test_n10.rate
snpio/example_data/trees/test_n100.rate
snpio/example_data/trees/test_n50.rate
snpio/example_data/trees/test_n500.rate
snpio/example_data/trees/test_siterates.txt
snpio/example_data/trees/test_siterates_n10.txt
snpio/example_data/trees/test_siterates_n100.txt
snpio/example_data/trees/test_siterates_n500.txt
snpio/example_data/vcf_files/nremover_test.vcf.gz
snpio/example_data/vcf_files/nremover_test.vcf.gz.tbi
snpio/example_data/vcf_files/nremover_test_copy.vcf
snpio/example_data/vcf_files/phylogen_subset14K.vcf
snpio/example_data/vcf_files/phylogen_subset14K.vcf.gz
snpio/example_data/vcf_files/phylogen_subset14K.vcf.gz.tbi
snpio/example_data/vcf_files/phylogen_subset14K.vcf_sorted.vcf.gz
snpio/example_data/vcf_files/phylogen_subset14K.vcf_sorted.vcf.gz.tbi
snpio/example_data/vcf_files/phylogen_subset14K_sorted.vcf
snpio/example_data/vcf_files/phylogen_subset14K_sorted.vcf.gz
snpio/example_data/vcf_files/phylogen_subset14K_sorted.vcf.gz.tbi
snpio/example_data/vcf_files/phylogen_subset3K.vcf
snpio/example_data/vcf_files/phylogen_subset3K.vcf.gz
snpio/example_data/vcf_files/phylogen_subset3K.vcf.gz.tbi
snpio/example_data/vcf_files/test_data.vcf.gz
snpio/example_data/vcf_files/test_data.vcf.gz.tbi
snpio/filtering/__init__.py
snpio/filtering/filtering_helper.py
snpio/filtering/filtering_methods.py
snpio/filtering/nremover2.py
snpio/img/d_statistics_distribution.png
snpio/img/d_statistics_significance_counts.png
snpio/img/filtering_results_bool.png
snpio/img/filtering_results_mac.png
snpio/img/filtering_results_maf.png
snpio/img/filtering_results_missing_loci_samples.png
snpio/img/filtering_results_missing_population.png
snpio/img/fst_between_populations_heatmap.png
snpio/img/missingness_report.png
snpio/img/nei_between_populations_heatmap.png
snpio/img/neis_genetic_distance.png
snpio/img/nremover_sankey_plot.png
snpio/img/outlier_snps_heatmap.png
snpio/img/pca_missingness.png
snpio/img/population_counts.png
snpio/img/snpio_code_flow_diagram.png
snpio/img/snpio_code_flow_diagram_1990s_retro.png
snpio/img/snpio_logo.png
snpio/img/summary_statistics.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/plotting.py
snpio/popgenstats/__init__.py
snpio/popgenstats/amova.py
snpio/popgenstats/d_statistics.py
snpio/popgenstats/fst_distance.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/pop_gen_statistics.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/custom_exceptions.py
snpio/utils/logging.py
snpio/utils/misc.py
snpio/utils/missing_stats.py
snpio/utils/multiqc_reporter.py
snpio/utils/plot_queue.py
snpio/utils/results_exporter.py
snpio/utils/sequence_tools.py