435 lines
23 KiB
Text
435 lines
23 KiB
Text
bin/hyphy
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lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
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lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod
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lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
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lib/hyphy/GeneticCodes/Ciliate.cod
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lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
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lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod
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lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod
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lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
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lib/hyphy/GeneticCodes/Mold_mtDNA.cod
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lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
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lib/hyphy/GeneticCodes/Vertebratemtdna.cod
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lib/hyphy/GeneticCodes/Yeast_mtDNA.cod
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lib/hyphy/SubstitutionClasses/AAEFV/Equal
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lib/hyphy/SubstitutionClasses/AAEFV/Estimated
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lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
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lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
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lib/hyphy/SubstitutionClasses/CodonEFV/Equal
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lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
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lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
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lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
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lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
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lib/hyphy/SubstitutionClasses/Heterogeneity/Beta
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lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
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lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
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lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
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lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
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lib/hyphy/SubstitutionClasses/NucEFV/Equal
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lib/hyphy/SubstitutionClasses/NucEFV/Estimated
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lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
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lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
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lib/hyphy/SubstitutionClasses/aa.bf
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lib/hyphy/SubstitutionClasses/codon.bf
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lib/hyphy/SubstitutionClasses/dinuc.bf
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lib/hyphy/SubstitutionClasses/nuc.bf
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lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
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lib/hyphy/SubstitutionModels/Binary/F81.mdl
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lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
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lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
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lib/hyphy/SubstitutionModels/User/Nucleotide/JC69
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lib/hyphy/SubstitutionModels/User/Nucleotide/K2P
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
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lib/hyphy/TemplateBatchFiles/AAModelComparison.bf
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lib/hyphy/TemplateBatchFiles/AddABias.ibf
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lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
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lib/hyphy/TemplateBatchFiles/BGM.bf
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lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
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lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf
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lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
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lib/hyphy/TemplateBatchFiles/CleanGaps.bf
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lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf
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lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
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lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
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lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
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lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf
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lib/hyphy/TemplateBatchFiles/CodonToProtein.bf
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lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf
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lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf
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lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def
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lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
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lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
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lib/hyphy/TemplateBatchFiles/Distances/JC69
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lib/hyphy/TemplateBatchFiles/Distances/K2P
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lib/hyphy/TemplateBatchFiles/Distances/K2P_RV
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lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
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lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
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lib/hyphy/TemplateBatchFiles/Distances/PC
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lib/hyphy/TemplateBatchFiles/Distances/PC_MH
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lib/hyphy/TemplateBatchFiles/Distances/PC_RV
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lib/hyphy/TemplateBatchFiles/Distances/T3P
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lib/hyphy/TemplateBatchFiles/Distances/TN84
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lib/hyphy/TemplateBatchFiles/Distances/TN93
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lib/hyphy/TemplateBatchFiles/Distances/TN93_RV
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lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
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lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
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lib/hyphy/TemplateBatchFiles/F_ST.bf
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lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf
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lib/hyphy/TemplateBatchFiles/GARD.bf
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lib/hyphy/TemplateBatchFiles/GA_CHC.ibf
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lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
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lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
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lib/hyphy/TemplateBatchFiles/Gateaux.bf
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lib/hyphy/TemplateBatchFiles/GateauxMR.bf
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lib/hyphy/TemplateBatchFiles/KHTest.bf
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lib/hyphy/TemplateBatchFiles/LEISR.bf
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lib/hyphy/TemplateBatchFiles/LHT.bf
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lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf
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lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf
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lib/hyphy/TemplateBatchFiles/LocalMolClock.bf
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lib/hyphy/TemplateBatchFiles/MGvsGY.bf
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lib/hyphy/TemplateBatchFiles/MergeSequences.bf
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lib/hyphy/TemplateBatchFiles/MergeSites.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
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lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
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lib/hyphy/TemplateBatchFiles/ModelTest.bf
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lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
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lib/hyphy/TemplateBatchFiles/MolecularClock.bf
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lib/hyphy/TemplateBatchFiles/NeighborJoining.bf
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lib/hyphy/TemplateBatchFiles/NielsenYang.bf
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lib/hyphy/TemplateBatchFiles/NucModelCompare.bf
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lib/hyphy/TemplateBatchFiles/PARRIS.bf
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lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
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lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
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lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
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lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
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lib/hyphy/TemplateBatchFiles/RelativeRate.bf
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lib/hyphy/TemplateBatchFiles/RelativeRatio.bf
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lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf
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lib/hyphy/TemplateBatchFiles/SGEmulator.bf
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lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
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lib/hyphy/TemplateBatchFiles/SGIvL.bf
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lib/hyphy/TemplateBatchFiles/SM-2019.bf
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lib/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf
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lib/hyphy/TemplateBatchFiles/Samplers/lhc.bf
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lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
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lib/hyphy/TemplateBatchFiles/Samplers/sir.bf
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lib/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf
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lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf
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lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-contrast.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
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lib/hyphy/TemplateBatchFiles/SelectionLRT.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
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lib/hyphy/TemplateBatchFiles/SequentialAddition.bf
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lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf
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lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf
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lib/hyphy/TemplateBatchFiles/SimmondsAI.bf
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lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
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lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
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lib/hyphy/TemplateBatchFiles/TemplateModels/190
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lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
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lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Default
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
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lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
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lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
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lib/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf
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lib/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/PCH
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16A
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNAF81
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV
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lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1
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lib/hyphy/TemplateBatchFiles/TemplateModels/S4
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lib/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def
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lib/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
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lib/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
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lib/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/models.lst
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lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
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