.zenodo.json
AUTHORS.rst
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.rst
DEV_NOTES.md
LICENSE
MANIFEST.in
NEWS.md
README.rst
SECURITY.md
pyproject.toml
setup.py
src/PyPop/Arlequin.py
src/PyPop/CommandLineInterface.py
src/PyPop/DataTypes.py
src/PyPop/Filter.py
src/PyPop/GUIApp.py
src/PyPop/Haplo.py
src/PyPop/HardyWeinberg.py
src/PyPop/Homozygosity.py
src/PyPop/Main.py
src/PyPop/Meta.py
src/PyPop/ParseFile.py
src/PyPop/RandomBinning.py
src/PyPop/Utils.py
src/PyPop/__init__.py
src/PyPop/_version.py
src/PyPop/popmeta.py
src/PyPop/pypop.py
src/PyPop/xslt/__init__.py
src/PyPop/xslt/allelelist-by-locus.xsl
src/PyPop/xslt/cdv.xsl
src/PyPop/xslt/common.xsl
src/PyPop/xslt/disease.xsl
src/PyPop/xslt/emhaplofreq.xsl
src/PyPop/xslt/filter.xsl
src/PyPop/xslt/haplolist-by-group.xsl
src/PyPop/xslt/haplos-to-count.xsl
src/PyPop/xslt/hardyweinberg.xsl
src/PyPop/xslt/homozygosity.xsl
src/PyPop/xslt/html.xsl
src/PyPop/xslt/lib.xsl
src/PyPop/xslt/meta-to-tsv.xsl
src/PyPop/xslt/nodeset.xsl
src/PyPop/xslt/phylip-allele.xsl
src/PyPop/xslt/phylip-haplo.xsl
src/PyPop/xslt/sort-by-locus.xsl
src/PyPop/xslt/summary.xsl
src/PyPop/xslt/text.xsl
src/PyPop/xslt/xsl.ced
src/PyPop/xslt/xsl.dtd
src/SWIG/typemap.i
src/emhaplofreq/ChangeLog
src/emhaplofreq/Makefile
src/emhaplofreq/drand48.c
src/emhaplofreq/emhaplofreq.c
src/emhaplofreq/emhaplofreq.h
src/emhaplofreq/emhaplofreq_OLD.c
src/emhaplofreq/emhaplofreq_wrap.i
src/emhaplofreq/test-guarani.dat
src/emhaplofreq/test-high-polymorphism.dat
src/emhaplofreq/test.dat
src/emhaplofreq/test.pop
src/emhaplofreq/test.py
src/emhaplofreq/test_nomiss.dat
src/emhaplofreq/test_nomiss.pop
src/gthwe/ChangeLog
src/gthwe/Makefile
src/gthwe/README.1
src/gthwe/cal_const.c
src/gthwe/cal_n.c
src/gthwe/cal_prob.c
src/gthwe/check_file.c
src/gthwe/do_switch.c
src/gthwe/example-2alleles.dat
src/gthwe/example-2alleles.gtout
src/gthwe/example.dat
src/gthwe/example.gtout
src/gthwe/func.h
src/gthwe/gthwe_wrap.i
src/gthwe/hwe.c
src/gthwe/hwe.h
src/gthwe/ln_p_value.c
src/gthwe/new_rand.c
src/gthwe/paiwan-test.dat
src/gthwe/print_data.c
src/gthwe/random_choose.c
src/gthwe/read_data.c
src/gthwe/select_index.c
src/gthwe/stamp_time.c
src/gthwe/statistics.c
src/gthwe/test_switch.c
src/gthwe/to_calculate_log.c
src/haplo-stats/Makefile
src/haplo-stats/README.md
src/haplo-stats/haplo_em_pin.c
src/haplo-stats/haplo_em_pin.h
src/haplo-stats/haplostats_wrap.i
src/haplo-stats/test1.py
src/haplo-stats/test2.py
src/haplo-stats/test3.py
src/haplo-stats/test4.py
src/pval/Makefile
src/pval/Rconfig.h
src/pval/Rmath.h
src/pval/bd0.c
src/pval/chebyshev.c
src/pval/comparison-r-code-vs-num-recipes.txt
src/pval/dnorm.c
src/pval/dpois.c
src/pval/dpq.h
src/pval/fmax2.c
src/pval/fmin2.c
src/pval/ftrunc.c
src/pval/gamma.c
src/pval/lgamma.c
src/pval/lgammacor.c
src/pval/mlutils.c
src/pval/nmath.h
src/pval/pchisq.c
src/pval/pgamma.c
src/pval/pnorm.c
src/pval/pval.c
src/pval/pval_wrap.i
src/pval/stirlerr.c
src/pval/R_ext/Arith.h
src/pval/R_ext/Boolean.h
src/pval/R_ext/Error.h
src/pval/R_ext/Mathlib.h
src/pval/R_ext/RS.h
src/pypop_genomics.egg-info/PKG-INFO
src/pypop_genomics.egg-info/SOURCES.txt
src/pypop_genomics.egg-info/dependency_links.txt
src/pypop_genomics.egg-info/entry_points.txt
src/pypop_genomics.egg-info/requires.txt
src/pypop_genomics.egg-info/top_level.txt
src/slatkin-exact/ChangeLog
src/slatkin-exact/Makefile
src/slatkin-exact/README
src/slatkin-exact/enumerate.c
src/slatkin-exact/monte-carlo.c
src/slatkin-exact/monte-carlo_wrap.i
tests/base.py
tests/conftest.py
tests/test_100k_Emhaplofreq.py
tests/test_AlleleColon.py
tests/test_Filters.py
tests/test_GenerateTSV.py
tests/test_GenotypeCommon.py
tests/test_Haplostats.py
tests/test_ManyOptions.py
tests/test_Popmeta.py
tests/test_StringMatrix.py
tests/test_USAFEL.py
tests/test_UserGuideExamples.py
tests/test_XSLT.py
tests/test_gthwe.py
tests/data/20loci.ini
tests/data/BIGDAWG_SynthControl_Data-out.xml
tests/data/BIGDAWG_SynthControl_Data.pop
tests/data/BIGDAWG_SynthControl_Data_dash-out.xml
tests/data/BIGDAWG_SynthControl_Data_dash.pop
tests/data/BIGDAWG_SynthControl_Data_with_metadata.pop
tests/data/Filters_CustomBinning_USAFEL.ini
tests/data/Filters_DigitBinning_USAFEL.ini
tests/data/HLANomen2010_Filter-test.pop
tests/data/HLANomen2010_hap.ini
tests/data/Synth_PyPop_Dataset.txt
tests/data/Test_100k_20loci_Dataset.ini
tests/data/Test_100k_20loci_Dataset.pop
tests/data/Test_Allele_Colon_Emhaplofreq.ini
tests/data/Test_Allele_Colon_Emhaplofreq.pop
tests/data/Test_Allele_Colon_HardyWeinberg.ini
tests/data/Test_Allele_Colon_HardyWeinberg.pop
tests/data/Test_LargerPopId_Haplostats.ini
tests/data/Test_Larger_Haplostats.ini
tests/data/Test_Larger_Haplostats.pop
tests/data/Test_Small_Haplostats.ini
tests/data/Test_Small_Haplostats.pop
tests/data/USAFEL-UchiTelle-small.pop
tests/data/WS_BDCtrl_Test_EM.ini
tests/data/WS_BDCtrl_Test_EM_2_locus.ini
tests/data/WS_BDCtrl_Test_EM_3_and_4_locus.ini
tests/data/WS_BDCtrl_Test_EM_4_locus.ini
tests/data/WS_BDCtrl_Test_EM_5_locus.ini
tests/data/WS_BDCtrl_Test_EM_plus_HW_2_locus.ini
tests/data/WS_BDCtrl_Test_HW.ini
tests/data/minimal-no-emhaplofreq-no-guothompson-no-slatkin.ini
tests/data/minimal-no-emhaplofreq-no-guothompson.ini
tests/data/minimal-no-emhaplofreq.ini
tests/data/minimal-with-permu.ini
tests/data/minimal.ini
tests/data/custom-binning-examples/G-Filter_config.ini
tests/data/custom-binning-examples/P-Filter_config.ini
tests/data/custom-binning-examples/many_options_config.ini
tests/data/doc-examples/config-minimal-example.ini
tests/data/doc-examples/data-allelecount.pop
tests/data/doc-examples/data-hla-microsat.pop
tests/data/doc-examples/data-hla.pop
tests/data/doc-examples/data-minimal-noheader-noids.pop
tests/data/doc-examples/data-minimal-noheader.pop
tests/data/doc-examples/data-nucleotide.pop
tests/data/gold-output/HLANomen2010_Filter-test-filter.xml
tests/data/gold-output/HLANomen2010_Filter-test-out.txt
tests/data/gold-output/USAFEL-UchiTelle-small-Filters_CustomBinning-out.txt
tests/data/gold-output/USAFEL-UchiTelle-small-Filters_DigitBinning-out.txt
tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson-no-slatkin.txt
tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson.txt
tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq.txt
tests/data/gold-output/USAFEL-UchiTelle-small-out.txt
tests/data/gold-output/USAFEL-UchiTelle-small-out.xml
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/1-locus-allele.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/1-locus-genotype.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/1-locus-hardyweinberg.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/1-locus-summary.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/2-locus-haplo.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/2-locus-summary.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/3-locus-haplo.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/3-locus-summary.tsv
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/USAFEL-UchiTelle-small-out.txt
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/USAFEL-UchiTelle-small-out.xml
tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/meta.xml
tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-filter.xml
tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-out.txt
tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-out.xml
tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-filter.xml
tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-out.txt
tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-out.xml
tests/data/gold-output/generate_tsv_2_locus/1-locus-allele.tsv
tests/data/gold-output/generate_tsv_2_locus/1-locus-summary.tsv
tests/data/gold-output/generate_tsv_2_locus/2-locus-haplo.tsv
tests/data/gold-output/generate_tsv_2_locus/2-locus-summary.tsv
tests/data/gold-output/generate_tsv_2_locus/meta.xml
tests/data/gold-output/generate_tsv_2_locus_with_HW/1-locus-allele.tsv
tests/data/gold-output/generate_tsv_2_locus_with_HW/1-locus-genotype.tsv
tests/data/gold-output/generate_tsv_2_locus_with_HW/1-locus-hardyweinberg.tsv
tests/data/gold-output/generate_tsv_2_locus_with_HW/1-locus-summary.tsv
tests/data/gold-output/generate_tsv_2_locus_with_HW/2-locus-haplo.tsv
tests/data/gold-output/generate_tsv_2_locus_with_HW/2-locus-summary.tsv
tests/data/gold-output/generate_tsv_2_locus_with_HW/meta.xml
tests/data/gold-output/generate_tsv_3_and_4_locus/1-locus-allele.tsv
tests/data/gold-output/generate_tsv_3_and_4_locus/1-locus-summary.tsv
tests/data/gold-output/generate_tsv_3_and_4_locus/3-locus-haplo.tsv
tests/data/gold-output/generate_tsv_3_and_4_locus/3-locus-summary.tsv
tests/data/gold-output/generate_tsv_3_and_4_locus/4-locus-haplo.tsv
tests/data/gold-output/generate_tsv_3_and_4_locus/4-locus-summary.tsv
tests/data/gold-output/generate_tsv_3_locus/1-locus-allele.tsv
tests/data/gold-output/generate_tsv_3_locus/1-locus-summary.tsv
tests/data/gold-output/generate_tsv_3_locus/3-locus-haplo.tsv
tests/data/gold-output/generate_tsv_3_locus/3-locus-summary.tsv
tests/data/gold-output/generate_tsv_3_locus/meta.xml
tests/data/gold-output/generate_tsv_4_locus/1-locus-allele.tsv
tests/data/gold-output/generate_tsv_4_locus/1-locus-summary.tsv
tests/data/gold-output/generate_tsv_4_locus/4-locus-haplo.tsv
tests/data/gold-output/generate_tsv_4_locus/4-locus-summary.tsv
tests/data/gold-output/generate_tsv_4_locus/meta.xml
tests/data/gold-output/generate_tsv_5_locus/1-locus-allele.tsv
tests/data/gold-output/generate_tsv_5_locus/1-locus-summary.tsv
tests/data/gold-output/generate_tsv_5_locus/5-locus-haplo.tsv
tests/data/gold-output/generate_tsv_5_locus/5-locus-summary.tsv
tests/data/gold-output/popmeta/1-locus-allele.tsv
tests/data/gold-output/popmeta/1-locus-pairwise-fnd.tsv
tests/data/gold-output/popmeta/1-locus-summary.tsv
tests/data/gold-output/popmeta/3-locus-haplo.tsv
tests/data/gold-output/popmeta/3-locus-summary.tsv
tests/data/gold-output/popmeta/meta.xml
tests/data/gold-output/popmeta_prefix/meta.xml
tests/data/gold-output/popmeta_prefix/prefix-1-locus-allele.tsv
tests/data/gold-output/popmeta_prefix/prefix-1-locus-pairwise-fnd.tsv
tests/data/gold-output/popmeta_prefix/prefix-1-locus-summary.tsv
tests/data/gold-output/popmeta_prefix/prefix-3-locus-haplo.tsv
tests/data/gold-output/popmeta_prefix/prefix-3-locus-summary.tsv