CMakeLists.txt
COPYING
MANIFEST.in
Makefile.in
README.rst
config.h.in
configure
setup.cfg
setup.py
setup.py.in
check_deps/Makefile
check_deps/test.cc
docs/Makefile
docs/conf.py
docs/conf.py.in
docs/index.rst
docs/references.bib
docs/_build/html/pyplots/tajd.py
docs/pages/changes.rst
docs/pages/deprecated_overview.rst
docs/pages/lifetimes.rst
docs/pages/summstats.rst
docs/pages/treesequences.rst
docs/pages/vmatrix.rst
docs/pages/zreferences.rst
docs/pyplots/tajd.py
libsequence/CMakeLists.txt
libsequence/__init__.py
libsequence/__main__.py
libsequence/citations.py
libsequence/msprime.py
libsequence/msstats_cli.py
libsequence/src/_libsequence.cc
libsequence/src/fst.cc
libsequence/src/omega_max.cc
libsequence/src/polytable.cc
libsequence/src/summstats.cc
libsequence/src/variant_matrix.cc
libsequence/src/windows_cpp.cc
libsequence/src/libsequence/Sequence/AlignStream.hpp
libsequence/src/libsequence/Sequence/Alignment.hpp
libsequence/src/libsequence/Sequence/AlleleCountMatrix.hpp
libsequence/src/libsequence/Sequence/Clustalw.hpp
libsequence/src/libsequence/Sequence/CodonTable.hpp
libsequence/src/libsequence/Sequence/Comeron95.hpp
libsequence/src/libsequence/Sequence/Comparisons.hpp
libsequence/src/libsequence/Sequence/ComplementBase.hpp
libsequence/src/libsequence/Sequence/CountingOperators.hpp
libsequence/src/libsequence/Sequence/FST.hpp
libsequence/src/libsequence/Sequence/Fasta.hpp
libsequence/src/libsequence/Sequence/Grantham.hpp
libsequence/src/libsequence/Sequence/GranthamWeights.hpp
libsequence/src/libsequence/Sequence/HKA.hpp
libsequence/src/libsequence/Sequence/Hudson2001.hpp
libsequence/src/libsequence/Sequence/Kimura80.hpp
libsequence/src/libsequence/Sequence/NonOwningCapsules.hpp
libsequence/src/libsequence/Sequence/PathwayHelper.hpp
libsequence/src/libsequence/Sequence/PolyFunctional.hpp
libsequence/src/libsequence/Sequence/PolySIM.hpp
libsequence/src/libsequence/Sequence/PolySNP.hpp
libsequence/src/libsequence/Sequence/PolySNPimpl.hpp
libsequence/src/libsequence/Sequence/PolySites.hpp
libsequence/src/libsequence/Sequence/PolyTable.hpp
libsequence/src/libsequence/Sequence/PolyTableFunctions.hpp
libsequence/src/libsequence/Sequence/PolyTableSlice.hpp
libsequence/src/libsequence/Sequence/Recombination.hpp
libsequence/src/libsequence/Sequence/RedundancyCom95.hpp
libsequence/src/libsequence/Sequence/Seq.hpp
libsequence/src/libsequence/Sequence/SeqAlphabets.hpp
libsequence/src/libsequence/Sequence/SeqConstants.hpp
libsequence/src/libsequence/Sequence/SeqEnums.hpp
libsequence/src/libsequence/Sequence/SeqFunctors.hpp
libsequence/src/libsequence/Sequence/SeqProperties.hpp
libsequence/src/libsequence/Sequence/SeqRegexes.hpp
libsequence/src/libsequence/Sequence/SeqUtilities.hpp
libsequence/src/libsequence/Sequence/SimData.hpp
libsequence/src/libsequence/Sequence/SimParams.hpp
libsequence/src/libsequence/Sequence/SimpleSNP.hpp
libsequence/src/libsequence/Sequence/SingleSub.hpp
libsequence/src/libsequence/Sequence/Sites.hpp
libsequence/src/libsequence/Sequence/StateCounts.hpp
libsequence/src/libsequence/Sequence/SummStatsDeprecated.hpp
libsequence/src/libsequence/Sequence/ThreeSubs.hpp
libsequence/src/libsequence/Sequence/Translate.hpp
libsequence/src/libsequence/Sequence/Translate2.hpp
libsequence/src/libsequence/Sequence/TwoSubs.hpp
libsequence/src/libsequence/Sequence/Unweighted.hpp
libsequence/src/libsequence/Sequence/VariantMatrix.hpp
libsequence/src/libsequence/Sequence/VariantMatrixCapsule.hpp
libsequence/src/libsequence/Sequence/VariantMatrixViews.hpp
libsequence/src/libsequence/Sequence/VectorCapsules.hpp
libsequence/src/libsequence/Sequence/WeightingSchemes.hpp
libsequence/src/libsequence/Sequence/bamreader.hpp
libsequence/src/libsequence/Sequence/bamrecord.hpp
libsequence/src/libsequence/Sequence/descriptiveStats.hpp
libsequence/src/libsequence/Sequence/fastq.hpp
libsequence/src/libsequence/Sequence/phylipData.hpp
libsequence/src/libsequence/Sequence/polySiteVector.hpp
libsequence/src/libsequence/Sequence/samflag.hpp
libsequence/src/libsequence/Sequence/samfunctions.hpp
libsequence/src/libsequence/Sequence/samrecord.hpp
libsequence/src/libsequence/Sequence/shortestPath.hpp
libsequence/src/libsequence/Sequence/stateCounter.hpp
libsequence/src/libsequence/Sequence/summstats.hpp
libsequence/src/libsequence/Sequence/typedefs.hpp
libsequence/src/libsequence/Sequence/Coalescent/Coalesce.hpp
libsequence/src/libsequence/Sequence/Coalescent/Coalescent.hpp
libsequence/src/libsequence/Sequence/Coalescent/DemographicModels.hpp
libsequence/src/libsequence/Sequence/Coalescent/FragmentsRescaling.hpp
libsequence/src/libsequence/Sequence/Coalescent/Initialize.hpp
libsequence/src/libsequence/Sequence/Coalescent/Mutation.hpp
libsequence/src/libsequence/Sequence/Coalescent/NeutralSample.hpp
libsequence/src/libsequence/Sequence/Coalescent/Recombination.hpp
libsequence/src/libsequence/Sequence/Coalescent/SimTypes.hpp
libsequence/src/libsequence/Sequence/Coalescent/Trajectories.hpp
libsequence/src/libsequence/Sequence/Coalescent/TreeOperations.hpp
libsequence/src/libsequence/Sequence/Coalescent/bits/Coalesce.tcc
libsequence/src/libsequence/Sequence/Coalescent/bits/DemographicModels.tcc
libsequence/src/libsequence/Sequence/Coalescent/bits/Mutation.tcc
libsequence/src/libsequence/Sequence/Coalescent/bits/Recombination.tcc
libsequence/src/libsequence/Sequence/Coalescent/bits/Trajectories.tcc
libsequence/src/libsequence/Sequence/SummStatsDeprecated/Garud.hpp
libsequence/src/libsequence/Sequence/SummStatsDeprecated/Snn.hpp
libsequence/src/libsequence/Sequence/SummStatsDeprecated/lHaf.hpp
libsequence/src/libsequence/Sequence/SummStatsDeprecated/nSL.hpp
libsequence/src/libsequence/Sequence/bits/AlignStream.tcc
libsequence/src/libsequence/Sequence/bits/Alignment.tcc
libsequence/src/libsequence/Sequence/bits/Clustalw.tcc
libsequence/src/libsequence/Sequence/bits/CountingOperators.tcc
libsequence/src/libsequence/Sequence/bits/PolySites.tcc
libsequence/src/libsequence/Sequence/bits/PolyTable.tcc
libsequence/src/libsequence/Sequence/bits/PolyTableFunctions.tcc
libsequence/src/libsequence/Sequence/bits/PolyTableSlice.tcc
libsequence/src/libsequence/Sequence/bits/Snn.tcc
libsequence/src/libsequence/Sequence/bits/col_view_iterator.hpp
libsequence/src/libsequence/Sequence/bits/descriptiveStats.tcc
libsequence/src/libsequence/Sequence/bits/phylipData.tcc
libsequence/src/libsequence/Sequence/bits/variant_matrix_views_internal.hpp
libsequence/src/libsequence/Sequence/summstats/algorithm.hpp
libsequence/src/libsequence/Sequence/summstats/allele_counts.hpp
libsequence/src/libsequence/Sequence/summstats/auxillary.hpp
libsequence/src/libsequence/Sequence/summstats/classics.hpp
libsequence/src/libsequence/Sequence/summstats/garud.hpp
libsequence/src/libsequence/Sequence/summstats/generic.hpp
libsequence/src/libsequence/Sequence/summstats/ld.hpp
libsequence/src/libsequence/Sequence/summstats/lhaf.hpp
libsequence/src/libsequence/Sequence/summstats/nSLiHS.hpp
libsequence/src/libsequence/Sequence/summstats/nsl.hpp
libsequence/src/libsequence/Sequence/summstats/nslx.hpp
libsequence/src/libsequence/Sequence/summstats/nvariablesites.hpp
libsequence/src/libsequence/Sequence/summstats/thetah.hpp
libsequence/src/libsequence/Sequence/summstats/thetal.hpp
libsequence/src/libsequence/Sequence/summstats/thetapi.hpp
libsequence/src/libsequence/Sequence/summstats/thetaw.hpp
libsequence/src/libsequence/Sequence/summstats/util.hpp
libsequence/src/libsequence/Sequence/variant_matrix/filtering.hpp
libsequence/src/libsequence/Sequence/variant_matrix/msformat.hpp
libsequence/src/libsequence/Sequence/variant_matrix/windows.hpp
libsequence/src/libsequence/examples/PolyTableIterators.cc
libsequence/src/libsequence/examples/baseComp.cc
libsequence/src/libsequence/examples/codons.cc
libsequence/src/libsequence/examples/correlations.cc
libsequence/src/libsequence/examples/int_handler.cc
libsequence/src/libsequence/examples/int_handler.hpp
libsequence/src/libsequence/examples/mean_nSLx.cc
libsequence/src/libsequence/examples/ms_to_VariantMatrix.cc
libsequence/src/libsequence/examples/msstats.cc
libsequence/src/libsequence/examples/nSL_from_ms.cc
libsequence/src/libsequence/examples/nSL_vs_nSLx.cc
libsequence/src/libsequence/examples/polySiteVector_test.cc
libsequence/src/libsequence/examples/slidingWindow.cc
libsequence/src/libsequence/examples/slidingWindow2.cc
libsequence/src/libsequence/examples/test_SimDataIO.cc
libsequence/src/libsequence/examples/translateTest.cc
libsequence/src/libsequence/examples/ufs.cc
libsequence/src/libsequence/examples/valid_dna.cc
libsequence/src/libsequence/src/CodonTable.cc
libsequence/src/libsequence/src/Comeron95.cc
libsequence/src/libsequence/src/Comparisons.cc
libsequence/src/libsequence/src/ComplementBase.cc
libsequence/src/libsequence/src/Grantham.cc
libsequence/src/libsequence/src/GranthamWeights.cc
libsequence/src/libsequence/src/Kimura80.cc
libsequence/src/libsequence/src/PathwayHelper.cc
libsequence/src/libsequence/src/PolySites.cc
libsequence/src/libsequence/src/PolyTable.cc
libsequence/src/libsequence/src/PolyTableFunctions.cc
libsequence/src/libsequence/src/PolyTableManip.cc
libsequence/src/libsequence/src/RedundancyCom95.cc
libsequence/src/libsequence/src/SeqAlphabets.cc
libsequence/src/libsequence/src/SeqConstants.cc
libsequence/src/libsequence/src/SimData.cc
libsequence/src/libsequence/src/SimParams.cc
libsequence/src/libsequence/src/SimpleSNP.cc
libsequence/src/libsequence/src/SingleSub.cc
libsequence/src/libsequence/src/Sites.cc
libsequence/src/libsequence/src/Specializations.cc
libsequence/src/libsequence/src/ThreeSubs.cc
libsequence/src/libsequence/src/Translate.cc
libsequence/src/libsequence/src/TwoSubs.cc
libsequence/src/libsequence/src/Unweighted.cc
libsequence/src/libsequence/src/libsequenceConfig.cc
libsequence/src/libsequence/src/polySiteVector.cc
libsequence/src/libsequence/src/shortestPath.cc
libsequence/src/libsequence/src/stateCounter.cc
libsequence/src/libsequence/src/Coalescent/CoalescentCoalesce.cc
libsequence/src/libsequence/src/Coalescent/CoalescentFragmentsRescaling.cc
libsequence/src/libsequence/src/Coalescent/CoalescentInitialize.cc
libsequence/src/libsequence/src/Coalescent/CoalescentMutation.cc
libsequence/src/libsequence/src/Coalescent/CoalescentRecombination.cc
libsequence/src/libsequence/src/Coalescent/CoalescentSimTypes.cc
libsequence/src/libsequence/src/Coalescent/CoalescentTreeOperations.cc
libsequence/src/libsequence/src/Seq/Fasta.cc
libsequence/src/libsequence/src/Seq/Seq.cc
libsequence/src/libsequence/src/Seq/fastq.cc
libsequence/src/libsequence/src/hts/bamreader.cc
libsequence/src/libsequence/src/hts/bamrecord.cc
libsequence/src/libsequence/src/hts/samflag.cc
libsequence/src/libsequence/src/hts/samfunctions.cc
libsequence/src/libsequence/src/hts/samrecord.cc
libsequence/src/libsequence/src/summstats/algorithm.hpp
libsequence/src/libsequence/src/summstats/allele_counts.cc
libsequence/src/libsequence/src/summstats/auxillary.cc
libsequence/src/libsequence/src/summstats/faywuh.cc
libsequence/src/libsequence/src/summstats/garud.cc
libsequence/src/libsequence/src/summstats/generic.cc
libsequence/src/libsequence/src/summstats/haplotype_statistics.cc
libsequence/src/libsequence/src/summstats/hprime.cc
libsequence/src/libsequence/src/summstats/hprime_faywuh_aggregator.hpp
libsequence/src/libsequence/src/summstats/ld.cc
libsequence/src/libsequence/src/summstats/lhaf.cc
libsequence/src/libsequence/src/summstats/nsl.cc
libsequence/src/libsequence/src/summstats/nsl_common.hpp
libsequence/src/libsequence/src/summstats/nslx.cc
libsequence/src/libsequence/src/summstats/nvariablesites.cc
libsequence/src/libsequence/src/summstats/rmin.cc
libsequence/src/libsequence/src/summstats/tajd.cc
libsequence/src/libsequence/src/summstats/thetah_thetal.cc
libsequence/src/libsequence/src/summstats/thetapi.cc
libsequence/src/libsequence/src/summstats/thetaw.cc
libsequence/src/libsequence/src/summstats_deprecated/FST.cc
libsequence/src/libsequence/src/summstats_deprecated/Garud.cc
libsequence/src/libsequence/src/summstats_deprecated/HKA.cc
libsequence/src/libsequence/src/summstats_deprecated/PolySIM.cc
libsequence/src/libsequence/src/summstats_deprecated/PolySNP.cc
libsequence/src/libsequence/src/summstats_deprecated/Recombination.cc
libsequence/src/libsequence/src/summstats_deprecated/Snn.cc
libsequence/src/libsequence/src/summstats_deprecated/SummStats.cc
libsequence/src/libsequence/src/summstats_deprecated/lHaf.cc
libsequence/src/libsequence/src/summstats_deprecated/nSL.cc
libsequence/src/libsequence/src/variant_matrix/AlleleCountMatrix.cc
libsequence/src/libsequence/src/variant_matrix/StateCounts.cc
libsequence/src/libsequence/src/variant_matrix/VariantMatrix.cc
libsequence/src/libsequence/src/variant_matrix/VariantMatrixViews.cc
libsequence/src/libsequence/src/variant_matrix/capsule.cc
libsequence/src/libsequence/src/variant_matrix/filtering.cc
libsequence/src/libsequence/src/variant_matrix/nonowningcapsules.cc
libsequence/src/libsequence/src/variant_matrix/windows.cc
libsequence/src/libsequence/test/AlignStreamTest.cc
libsequence/src/libsequence/test/AlignmentTest.cc
libsequence/src/libsequence/test/ComparisonsTest.cc
libsequence/src/libsequence/test/CountingOperators.cc
libsequence/src/libsequence/test/FastaConstructors.cc
libsequence/src/libsequence/test/FastaExplicitIO.cc
libsequence/src/libsequence/test/FastaIO.cc
libsequence/src/libsequence/test/FastaOperations.cc
libsequence/src/libsequence/test/PolySIMtest.cc
libsequence/src/libsequence/test/PolySNPtest.cc
libsequence/src/libsequence/test/PolySitesIO.cc
libsequence/src/libsequence/test/PolyTableBadBehavior.cc
libsequence/src/libsequence/test/PolyTableConversions.cc
libsequence/src/libsequence/test/PolyTableSliceTest.cc
libsequence/src/libsequence/test/PolyTableTweaking.cc
libsequence/src/libsequence/test/RedundancyCom95test.cc
libsequence/src/libsequence/test/Seq8test.cc
libsequence/src/libsequence/test/SeqConversions.cc
libsequence/src/libsequence/test/SimpleSNPIO.cc
libsequence/src/libsequence/test/VariantMatrixFixture.hpp
libsequence/src/libsequence/test/VariantMatrixTest.cc
libsequence/src/libsequence/test/alphabets.cc
libsequence/src/libsequence/test/fastqConstructors.cc
libsequence/src/libsequence/test/fastqIO.cc
libsequence/src/libsequence/test/libseq_unit_tests.cc
libsequence/src/libsequence/test/msformatdata.cc
libsequence/src/libsequence/test/msformatdata.hpp
libsequence/src/libsequence/test/msprime_data_fixture.hpp
libsequence/src/libsequence/test/polySiteVectorTest.cc
libsequence/src/libsequence/test/stateCounterTest.cc
libsequence/src/libsequence/test/testAlleleCountMatrix.cc
libsequence/src/libsequence/test/testClassicSummstats.cc
libsequence/src/libsequence/test/testClassicSummstatsEmptyVariantMatrix.cc
libsequence/src/libsequence/test/testGarudStatistics.cc
libsequence/src/libsequence/test/testLD.cc
libsequence/src/libsequence/test/testVariantMatrixWindows.cc
m4/ax_cxx_compile_stdxx_11.m4
m4/python.m4
pylibseq.egg-info/PKG-INFO
pylibseq.egg-info/SOURCES.txt
pylibseq.egg-info/dependency_links.txt
pylibseq.egg-info/not-zip-safe
pylibseq.egg-info/requires.txt
pylibseq.egg-info/top_level.txt
tests/__init__.py
tests/test_AlleleCountMatrix.py
tests/test_StateCounter.py
tests/test_VariantMatrix.py
tests/test_fst.py
tests/test_polytable.py
tests/test_summstats.py
tests/test_windows.py