COPYING
GPL.txt
LICENSE
MANIFEST.in
README.rst
setup.py
EggLib.egg-info/PKG-INFO
EggLib.egg-info/SOURCES.txt
EggLib.egg-info/dependency_links.txt
EggLib.egg-info/not-zip-safe
EggLib.egg-info/requires.txt
EggLib.egg-info/top_level.txt
doc/logo/banner.png
packaging/compile.py
src/cppfiles/AlleleStatus.cpp
src/cppfiles/AlleleStatus.hpp
src/cppfiles/Alphabet.cpp
src/cppfiles/Alphabet.epp
src/cppfiles/Alphabet.hpp
src/cppfiles/BED.cpp
src/cppfiles/BED.hpp
src/cppfiles/Coalesce.cpp
src/cppfiles/Coalesce.hpp
src/cppfiles/ComputeV.cpp
src/cppfiles/ComputeV.hpp
src/cppfiles/DataHolder.cpp
src/cppfiles/DataHolder.hpp
src/cppfiles/Diversity1.cpp
src/cppfiles/Diversity1.hpp
src/cppfiles/Diversity2.cpp
src/cppfiles/Diversity2.hpp
src/cppfiles/EHH.cpp
src/cppfiles/EHH.hpp
src/cppfiles/Exception.cpp
src/cppfiles/Export.cpp
src/cppfiles/Export.hpp
src/cppfiles/Fasta.cpp
src/cppfiles/Fasta.hpp
src/cppfiles/FreqHolder.cpp
src/cppfiles/FreqHolder.hpp
src/cppfiles/Fs.cpp
src/cppfiles/Fs.hpp
src/cppfiles/GFF3.cpp
src/cppfiles/GFF3.hpp
src/cppfiles/GeneticCode.cpp
src/cppfiles/GeneticCode.epp
src/cppfiles/GeneticCode.hpp
src/cppfiles/Genotypes.cpp
src/cppfiles/Genotypes.hpp
src/cppfiles/Haplotypes.cpp
src/cppfiles/Haplotypes.hpp
src/cppfiles/LD.cpp
src/cppfiles/LD.hpp
src/cppfiles/Lineage.cpp
src/cppfiles/Lineage.hpp
src/cppfiles/ParalogPi.cpp
src/cppfiles/ParalogPi.hpp
src/cppfiles/Params.cpp
src/cppfiles/Params.hpp
src/cppfiles/Random.cpp
src/cppfiles/Random.hpp
src/cppfiles/Rd.cpp
src/cppfiles/Rd.hpp
src/cppfiles/SiteDiversity.cpp
src/cppfiles/SiteDiversity.hpp
src/cppfiles/SiteHolder.cpp
src/cppfiles/SiteHolder.hpp
src/cppfiles/Structure.cpp
src/cppfiles/Structure.hpp
src/cppfiles/Tree.cpp
src/cppfiles/Tree.hpp
src/cppfiles/VCF.cpp
src/cppfiles/VCF.hpp
src/cppfiles/VcfIndex.cpp
src/cppfiles/VcfIndex.hpp
src/cppfiles/VcfWindow.cpp
src/cppfiles/VcfWindow.hpp
src/cppfiles/egglib.hpp
src/cppfiles/eggwrapper.cpp
src/cppfiles/stirling.hpp
src/egglib/__init__.py
src/egglib/_freq.py
src/egglib/_interface.py
src/egglib/_site.py
src/egglib/_tree.py
src/egglib/alphabets.py
src/egglib/eggwrapper.py
src/egglib/random.py
src/egglib/coalesce/__init__.py
src/egglib/coalesce/_param_helpers.py
src/egglib/coalesce/_simulator.py
src/egglib/io/__init__.py
src/egglib/io/_fasta.py
src/egglib/io/_genbank.py
src/egglib/io/_genepop.py
src/egglib/io/_gff3.py
src/egglib/io/_legacy.py
src/egglib/io/_ms.py
src/egglib/io/_vcf.py
src/egglib/stats/__init__.py
src/egglib/stats/_baudry.py
src/egglib/stats/_coding_diversity.py
src/egglib/stats/_cstats.py
src/egglib/stats/_ehh.py
src/egglib/stats/_haplotypes.py
src/egglib/stats/_ld.py
src/egglib/stats/_paralog_pi.py
src/egglib/tools/__init__.py
src/egglib/tools/_code_tools.py
src/egglib/tools/_concat.py
src/egglib/tools/_reading_frame.py
src/egglib/tools/_seq_manip.py
src/egglib/tools/_to_codons.py
src/egglib/wrappers/__init__.py
src/egglib/wrappers/_blast.py
src/egglib/wrappers/_clustal.py
src/egglib/wrappers/_codeml.py
src/egglib/wrappers/_muscle.py
src/egglib/wrappers/_nj.py
src/egglib/wrappers/_phyml.py
src/egglib/wrappers/_utils.py
test/__main__.py
test/test_modules/__init__.py
test/test_modules/test_base/__init__.py
test/test_modules/test_base/test_alphabet.py
test/test_modules/test_base/test_base.py
test/test_modules/test_base/test_misc.py
test/test_modules/test_base/test_site.py
test/test_modules/test_base/test_structure.py
test/test_modules/test_base/test_tree.py
test/test_modules/test_base/correct_files/test_aln_to_fasta.fa
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test/test_modules/test_base/correct_files/test_cnt_to_fasta.fa
test/test_modules/test_base/correct_files/test_cnt_to_fasta_.fa
test/test_modules/test_base/correct_files/test_to_fasta.fa
test/test_modules/test_base/correct_files/test_to_fasta_.fa
test/test_modules/test_coalesce/__init__.py
test/test_modules/test_coalesce/test_param_helpers.py
test/test_modules/test_coalesce/test_simulator.py
test/test_modules/test_io/__init__.py
test/test_modules/test_io/test_fasta.py
test/test_modules/test_io/test_genbank.py
test/test_modules/test_io/test_genepop.py
test/test_modules/test_io/test_gff3.py
test/test_modules/test_io/test_index.py
test/test_modules/test_io/test_legacy.py
test/test_modules/test_io/test_ms.py
test/test_modules/test_io/test_vcf.py
test/test_modules/test_io/tri.py
test/test_modules/test_io/correct_files/CEU.exon.2010_03.genotypes.vcf
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test/test_modules/test_io/correct_files/scaffold_285.vcf
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test/test_modules/test_io/correct_files/tmp_vcf.vcf
test/test_modules/test_io/correct_files/vcfw_vcf.py
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test/test_modules/test_stats/test_coding_diversity.py
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test/test_modules/test_stats/test_ehh.py
test/test_modules/test_stats/test_freq.py
test/test_modules/test_stats/test_haplotypes.py
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