data/hyphy-2.5.23+dfsg/.coveralls.condarc: ASCII text data/hyphy-2.5.23+dfsg/.coveralls.env.yml: ASCII text data/hyphy-2.5.23+dfsg/.gitattributes: ASCII text data/hyphy-2.5.23+dfsg/.github/workflows/benchmark.yml: ASCII text, with CRLF line terminators data/hyphy-2.5.23+dfsg/.github/workflows/coverage.yml: ASCII text data/hyphy-2.5.23+dfsg/.github/workflows/release.yml: ASCII text data/hyphy-2.5.23+dfsg/.github/workflows/stale.yml: ASCII text data/hyphy-2.5.23+dfsg/.travis.yml: ASCII text data/hyphy-2.5.23+dfsg/CONTRIBUTING.md: ASCII text data/hyphy-2.5.23+dfsg/Examples/BatchLanguage/MatrixIndexing.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/BatchLanguage/profile_test.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Categories/data/aspectrin.nuc: ASCII text, with very long lines, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Categories/definitions+MLE.bf: ASCII text, with CR line terminators 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ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/DataFilters/HKY852blocks2models.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/DataFilters/data/actin2.flt: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/ExonIntron.bf: ASCII text, with very long lines, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/Models/EI.mdl: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/Models/MG94x2.mdl: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/aa.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/data/3.seq: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/data/stewart.aa: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/MoreComplexModels/data/ubiq.flt: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/F81.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/HKY85.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/HKY85shared.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/JC69.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/K2P.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/K2Pshared.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/Non-Rev.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/REV.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/REVshared.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleAnalyses/data/hiv.nuc: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/F81K81uf_relratio.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/F81relrate.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/F81relratio.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/HKY85relrate.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/HKY85relratio.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/MolecularClockF81.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/MolecularClockHKY85.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/data/3.seq: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/data/aspectrin1.nuc: ASCII text, with very long lines, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/data/aspectrin2.nuc: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/SimpleConstraints/data/molclock.seq: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Simulation/PBootstrapHetRates.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Simulation/ParametricBootstrap.bf: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Simulation/RelativeRatePBS.bf: ASCII text, with very long lines, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Simulation/data/3.seq: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/Examples/Simulation/data/hiv.nuc: ASCII text, with CR line terminators data/hyphy-2.5.23+dfsg/LICENSE: ASCII text data/hyphy-2.5.23+dfsg/README.md: ASCII text, with very long lines data/hyphy-2.5.23+dfsg/bench.js: ASCII text, with CRLF line terminators data/hyphy-2.5.23+dfsg/cmake/FindOpenCL.cmake: ASCII text data/hyphy-2.5.23+dfsg/cmake/cmake_uninstall.cmake.in: ASCII text data/hyphy-2.5.23+dfsg/contrib/cl2hdr.c: C source, ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Alt_Yeast_Nuclear.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Ascidian_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Blepharisma_Nuclear.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Ciliate.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Echinoderm_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Euplotid_Nuclear.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Flatworm_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Invertebrate_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Mold_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Thraustochytrium_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Vertebratemtdna.cod: ASCII text data/hyphy-2.5.23+dfsg/res/GeneticCodes/Yeast_mtDNA.cod: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/AAEFV/Equal: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/AAEFV/Estimated: ASCII text, with very long lines data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/AAEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/AAEFV/Observed' (No such file or directory) In: cannot open `In' (No such file or directory) Data: cannot open `Data' (No such file or directory) Set: cannot open `Set' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/AAEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/AAEFV/Observed' (No such file or directory) In: cannot open `In' (No such file or directory) Partition: cannot open `Partition' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Equal: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Observed' (No such file or directory) Codon: cannot open `Codon' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Observed' (No such file or directory) Nuc: cannot open `Nuc' (No such file or directory) 3: cannot open `3' (No such file or directory) params.: cannot open `params.' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/CodonEFV/Observed' (No such file or directory) Nuc: cannot open `Nuc' (No such file or directory) 9: cannot open `9' (No such file or directory) params.: cannot open `params.' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/2: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/2' (No such file or directory) Bin: cannot open `Bin' (No such file or directory) Discrete: cannot open `Discrete' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/Beta: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/Beta-Gamma: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/General: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/General' (No such file or directory) Discrete: cannot open `Discrete' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/Half: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/Half' (No such file or directory) Normal: cannot open `Normal' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/Heterogeneity/Lognormal: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/NucEFV/Equal: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/NucEFV/Estimated: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/NucEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/NucEFV/Observed' (No such file or directory) In: cannot open `In' (No such file or directory) Data: cannot open `Data' (No such file or directory) Set: cannot open `Set' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/NucEFV/Observed: cannot open `data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/NucEFV/Observed' (No such file or directory) In: cannot open `In' (No such file or directory) Partition: cannot open `Partition' (No such file or directory) data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/aa.bf: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/codon.bf: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/dinuc.bf: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionClasses/nuc.bf: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Aminoacid/Dayhoff.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Aminoacid/EIAA.mdl: ASCII text, with very long lines data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Aminoacid/Fitness.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Aminoacid/Jones.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Aminoacid/mtREV.mdl: ASCII text, with very long lines data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Binary/F81.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/GY94_3x4.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94_3x4.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94_REV_3x4.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Codon/MG94xTN93_3x4.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Nucleotide/EFVEstimated.ibf: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Nucleotide/F81.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Nucleotide/HKY85.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Nucleotide/REV.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Nucleotide/REVBetaGamma.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/Nucleotide/TrN.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/User/Nucleotide/JC69: ASCII text data/hyphy-2.5.23+dfsg/res/SubstitutionModels/User/Nucleotide/K2P: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/GY94.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/gamma1.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/2RatesAnalyses/gamma2.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/AAModelComparison.bf: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/AddABias.ibf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/AnalyzeCodonData.bf: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/AnalyzeDiNucData.bf: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/AnalyzeNucDataFreq.bf: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/AnalyzeNucProtData.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/BGM.bf: C++ source, UTF-8 Unicode text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/BivariateCodonRateAnalysis.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/BranchSiteREL.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/BranchSiteRELMultiModel.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/CleanGaps.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/CleanStopCodons.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/ClusterAnalysis.bf: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/ClusterByDistanceRange.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/CodonBivariateRateProcessor.bf: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/CodonModelCompare.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/CodonToProtein.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/ConvertDataFile.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/DistanceMatrix.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/CodonTools.def: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/CodonTools2.def: C source, ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/CodonToolsMain.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/JC69: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/K2P: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/K2P_RV: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/Modified_Nei_Gojobori: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/Nei_Gojobori: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/PC: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/PC_MH: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/PC_RV: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/T3P: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/TN84: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/TN93: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/TN93_RV: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/Unaligned_LZ: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/Unaligned_LZ_FR: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/p_Distance: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/p_Distance_aa: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/p_Distance_binary: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Distances/p_Distance_codon: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/F_ST.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/FitnessAAModels.bf: CSV text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/GARD.bf: UTF-8 Unicode text, with very long lines data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/GA_CHC.ibf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/GA_CHC_Binary.ibf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/GUI/crayolaColors.def: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/Gateaux.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/GateauxMR.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/KHTest.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/LEISR.bf: UTF-8 Unicode text, with very long lines data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/LHT.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/LRTRecombTest.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/LZ_Complexity.bf: ASCII text data/hyphy-2.5.23+dfsg/res/TemplateBatchFiles/LocalMolClock.bf: C source, ASCII 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