COPYING
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
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/_export.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/_discretize.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
test/test_modules/test_base/correct_files/test_aln_to_fasta_.fa
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
test/test_modules/test_io/correct_files/MtChr2_315000-415000.gb
test/test_modules/test_io/correct_files/Osativa_193_gene_shortened.gff3
test/test_modules/test_io/correct_files/Osativa_193_gene_thinned.gff3
test/test_modules/test_io/correct_files/Populus_trichocarpa_short.gff3
test/test_modules/test_io/correct_files/Populus_trichocarpa_short_thinned.gff3
test/test_modules/test_io/correct_files/a.gff3
test/test_modules/test_io/correct_files/a.vcf
test/test_modules/test_io/correct_files/align.aln
test/test_modules/test_io/correct_files/align1_T.fas
test/test_modules/test_io/correct_files/b.gff3
test/test_modules/test_io/correct_files/example.fg
test/test_modules/test_io/correct_files/example.gnl
test/test_modules/test_io/correct_files/example.sta
test/test_modules/test_io/correct_files/genepop1.txt
test/test_modules/test_io/correct_files/genepop2.txt
test/test_modules/test_io/correct_files/human_fragment.bed
test/test_modules/test_io/correct_files/human_fragment.vcf
test/test_modules/test_io/correct_files/human_fragment.vcfi
test/test_modules/test_io/correct_files/merged_filt_depth_75_200_ssduplicateindANDsnp-ssblanck_DEF_for_structure.vcf
test/test_modules/test_io/correct_files/merged_filt_depth_75_200_ssduplicateindANDsnp-ssblanck_DEF_for_structure.vcfi
test/test_modules/test_io/correct_files/scaffold_285.vcf
test/test_modules/test_io/correct_files/thin.py
test/test_modules/test_io/correct_files/tmp_HF_GL.vcf
test/test_modules/test_io/correct_files/tmp_HF_GL.vcfi
test/test_modules/test_io/correct_files/tmp_MFD75200_PL.vcf
test/test_modules/test_io/correct_files/tmp_MFD75200_PL.vcfi
test/test_modules/test_io/correct_files/tmp_vcf.vcf
test/test_modules/test_io/correct_files/vcfw_vcf.py
test/test_modules/test_io/erroneous_files/align1_E.fas
test/test_modules/test_io/erroneous_files/align1_F.fas
test/test_modules/test_io/erroneous_files/clustal_error1.aln
test/test_modules/test_io/erroneous_files/clustal_error2.aln
test/test_modules/test_io/erroneous_files/clustal_error3.aln
test/test_modules/test_io/erroneous_files/clustal_error4.aln
test/test_modules/test_io/erroneous_files/clustal_error5.aln
test/test_modules/test_io/erroneous_files/clustal_error6.aln
test/test_modules/test_io/erroneous_files/clustal_error7.aln
test/test_modules/test_io/erroneous_files/clustal_error8.aln
test/test_modules/test_io/erroneous_files/clustal_error9.aln
test/test_modules/test_io/erroneous_files/example_E.fg
test/test_modules/test_io/erroneous_files/example_E.sta
test/test_modules/test_io/erroneous_files/example_E2.fg
test/test_modules/test_io/erroneous_files/example_E3.fg
test/test_modules/test_io/erroneous_files/exemple_E1.vcf
test/test_modules/test_io/erroneous_files/exemple_E2.vcf
test/test_modules/test_io/erroneous_files/exemple_N.vcf
test/test_modules/test_io/erroneous_files/genepop0.txt
test/test_modules/test_stats/__init__.py
test/test_modules/test_stats/test_baudry.py
test/test_modules/test_stats/test_coding_diversity.py
test/test_modules/test_stats/test_cstats.py
test/test_modules/test_stats/test_ehh.py
test/test_modules/test_stats/test_freq.py
test/test_modules/test_stats/test_haplotypes.py
test/test_modules/test_stats/test_ld.py
test/test_modules/test_stats/test_paralog_pi.py
test/test_modules/test_stats/test_site_diversity.py
test/test_modules/test_stats/control_stats/001-0006534.fas
test/test_modules/test_stats/control_stats/C94.gpop
test/test_modules/test_stats/control_stats/C94MD.gpop
test/test_modules/test_stats/control_stats/C98.gpop
test/test_modules/test_stats/control_stats/C98MD.gpop
test/test_modules/test_stats/control_stats/FTLa.fas
test/test_modules/test_stats/control_stats/FTLa_1.fas
test/test_modules/test_stats/control_stats/P93.gpop
test/test_modules/test_stats/control_stats/P93MD.gpop
test/test_modules/test_stats/control_stats/W08.gpop
test/test_modules/test_stats/control_stats/W08MD.gpop
test/test_modules/test_stats/control_stats/align001.fas
test/test_modules/test_stats/control_stats/align002.fas
test/test_modules/test_stats/control_stats/align003.fas
test/test_modules/test_stats/control_stats/align004.fas
test/test_modules/test_stats/control_stats/align005.fas
test/test_modules/test_stats/control_stats/align006.fas
test/test_modules/test_stats/control_stats/align007.fas
test/test_modules/test_stats/control_stats/bta12_cgu.hap
test/test_modules/test_stats/control_stats/bta12_cgu.inp
test/test_modules/test_stats/control_stats/dmi1.fas
test/test_modules/test_stats/control_stats/eIF4E.fas
test/test_modules/test_stats/control_stats/ehh_data01.hap
test/test_modules/test_stats/control_stats/ehh_data01.inp
test/test_modules/test_stats/control_stats/ehh_data02.hap
test/test_modules/test_stats/control_stats/ehh_data02.inp
test/test_modules/test_stats/control_stats/genepop001.txt
test/test_modules/test_stats/control_stats/genepop002.txt
test/test_modules/test_stats/control_stats/genepop003.txt
test/test_modules/test_stats/control_stats/lax4.fas
test/test_modules/test_stats/control_stats/simul001.fas
test/test_modules/test_stats/control_stats/simul002.fas
test/test_modules/test_stats/control_stats/simul003.fas
test/test_modules/test_stats/control_stats/simul004.fas
test/test_modules/test_stats/control_stats/simul005.fas
test/test_modules/test_stats/control_stats/simul006-no_multi.fas
test/test_modules/test_stats/control_stats/simul006-no_multi_in_1st_pair.fas
test/test_modules/test_stats/control_stats/simul006.fas
test/test_modules/test_stats/control_stats/simul007.fas
test/test_modules/test_stats/control_stats/simul008.fas
test/test_modules/test_stats/control_stats/simul009.fas
test/test_modules/test_stats/control_stats/simul010.fas
test/test_modules/test_stats/control_stats/simul011.fas
test/test_modules/test_stats/control_stats/simul012.fas
test/test_modules/test_stats/control_stats/simul013.fas
test/test_modules/test_stats/control_stats/simul014.fas
test/test_modules/test_stats/control_stats/sites001.txt
test/test_modules/test_stats/control_stats/sites002.txt
test/test_modules/test_stats/control_stats/sites003.txt
test/test_modules/test_stats/control_stats/sites004.txt
test/test_modules/test_stats/control_stats/stats.txt
test/test_modules/test_stats/control_stats/test001.fas
test/test_modules/test_stats/control_stats/unk29.fas
test/test_modules/test_stats/correct_files/50_seqs_100_100_bp.fas
test/test_modules/test_stats/correct_files/At-Ia.fas
test/test_modules/test_stats/correct_files/CR000837.1.fas
test/test_modules/test_stats/correct_files/Ia.aln.ugp.fas
test/test_modules/test_stats/correct_files/align1_T.fas
test/test_modules/test_stats/correct_files/codon_align.fas
test/test_modules/test_stats/correct_files/dmi3.fas
test/test_modules/test_stats/correct_files/example1.vcf
test/test_modules/test_stats/correct_files/example2.vcf
test/test_modules/test_stats/correct_files/my_file_f.vcf
test/test_modules/test_stats/correct_files/strepto_aln.fas
test/test_modules/test_stats/correct_files/strepto_aln.txt
test/test_modules/test_stats/erroneous_files/125_seqs_300_300_bp.fas
test/test_modules/test_stats/erroneous_files/At-Ia.fas
test/test_modules/test_stats/erroneous_files/c_file_1.fsa
test/test_modules/test_stats/erroneous_files/exemple1_F.vcf
test/test_modules/test_stats/erroneous_files/file_fail.fsa
test/test_modules/test_stats/erroneous_files/file_stop.fsa
test/test_modules/test_tools/__init__.py
test/test_modules/test_tools/prepare.py
test/test_modules/test_tools/stats_func.py
test/test_modules/test_tools/test_code_tools.py
test/test_modules/test_tools/test_concat.py
test/test_modules/test_tools/test_random.py
test/test_modules/test_tools/test_reading_frame.py
test/test_modules/test_tools/test_seq_manip.py
test/test_modules/test_tools/correct_files/LYK.cds
test/test_modules/test_tools/correct_files/LYK.prot.aln
test/test_modules/test_tools/correct_files/LYK.prot_nostop.aln
test/test_modules/test_tools/correct_files/align_generate.fsa
test/test_modules/test_tools/correct_files/c_file_1.1.fsa
test/test_modules/test_tools/correct_files/c_file_1.fsa
test/test_modules/test_tools/correct_files/c_file_2.fsa
test/test_modules/test_tools/correct_files/file_test.fa
test/test_modules/test_tools/correct_files/resultats_prot.txt
test/test_modules/test_tools/correct_files/sequence.fa
test/test_modules/test_tools/correct_files/traitement.sh
test/test_modules/test_tools/erroneous_files/LYK.E.cds
test/test_modules/test_tools/erroneous_files/LYK.E2.cds
test/test_modules/test_tools/erroneous_files/LYK.prot.E.aln
test/test_modules/test_tools/erroneous_files/LYK.prot.E2.aln
test/test_modules/test_tools/erroneous_files/LYK.prot_nostop.aln
test/test_modules/test_wrappers/__init__.py
test/test_modules/test_wrappers/test_alphabets.py
test/test_modules/test_wrappers/test_blast.py
test/test_modules/test_wrappers/test_clustal.py
test/test_modules/test_wrappers/test_codeml.py
test/test_modules/test_wrappers/test_muscle.py
test/test_modules/test_wrappers/test_nj.py
test/test_modules/test_wrappers/test_phyml.py
test/test_modules/test_wrappers/correct_files/Chr4.fa
test/test_modules/test_wrappers/correct_files/Chr4_prot.fa
test/test_modules/test_wrappers/correct_files/after_clustal
test/test_modules/test_wrappers/correct_files/cds.fas
test/test_modules/test_wrappers/correct_files/cds_clust.fas
test/test_modules/test_wrappers/correct_files/cicer_arietinum.fas
test/test_modules/test_wrappers/correct_files/codon_align.fas
test/test_modules/test_wrappers/correct_files/example.fas
test/test_modules/test_wrappers/correct_files/mask_nucl_dustmasker.asnb
test/test_modules/test_wrappers/correct_files/mask_nucl_windowmasker.asnb
test/test_modules/test_wrappers/correct_files/medicago_truncatula.fas
test/test_modules/test_wrappers/correct_files/mk_masks.sh
test/test_modules/test_wrappers/correct_files/nucl_data.fas
test/test_modules/test_wrappers/correct_files/prot_data.fas
test/test_modules/test_wrappers/correct_files/query_prot.fas
test/test_modules/test_wrappers/correct_files/simul-cds.fas
test/test_modules/test_wrappers/erroneous_files/cds_e.fas
test/test_modules/test_wrappers/erroneous_files/codon_align_cstop.fas
test/test_modules/test_wrappers/erroneous_files/error.fas
test/test_modules/test_wrappers/erroneous_files/error.txt
test/test_modules/test_wrappers/erroneous_files/example_Els.fas
test/test_modules/test_wrappers/erroneous_files/example_edpl.fas
test/test_modules/test_wrappers/erroneous_files/example_ename.fas