bin/hyphy
%%DATADIR%%/GeneticCodes/Alt_Yeast_Nuclear.cod
%%DATADIR%%/GeneticCodes/Ascidian_mtDNA.cod
%%DATADIR%%/GeneticCodes/Blepharisma_Nuclear.cod
%%DATADIR%%/GeneticCodes/Ciliate.cod
%%DATADIR%%/GeneticCodes/Echinoderm_mtDNA.cod
%%DATADIR%%/GeneticCodes/Euplotid_Nuclear.cod
%%DATADIR%%/GeneticCodes/Flatworm_mtDNA.cod
%%DATADIR%%/GeneticCodes/Invertebrate_mtDNA.cod
%%DATADIR%%/GeneticCodes/Mold_mtDNA.cod
%%DATADIR%%/GeneticCodes/Thraustochytrium_mtDNA.cod
%%DATADIR%%/GeneticCodes/Vertebratemtdna.cod
%%DATADIR%%/GeneticCodes/Yeast_mtDNA.cod
%%DATADIR%%/SubstitutionClasses/AAEFV/Equal
%%DATADIR%%/SubstitutionClasses/AAEFV/Estimated
%%DATADIR%%/SubstitutionClasses/AAEFV/Observed In Data Set
%%DATADIR%%/SubstitutionClasses/AAEFV/Observed In Partition
%%DATADIR%%/SubstitutionClasses/CodonEFV/Equal
%%DATADIR%%/SubstitutionClasses/CodonEFV/Observed Codon
%%DATADIR%%/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
%%DATADIR%%/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
%%DATADIR%%/SubstitutionClasses/Heterogeneity/2 Bin Discrete
%%DATADIR%%/SubstitutionClasses/Heterogeneity/Beta
%%DATADIR%%/SubstitutionClasses/Heterogeneity/Beta-Gamma
%%DATADIR%%/SubstitutionClasses/Heterogeneity/General Discrete
%%DATADIR%%/SubstitutionClasses/Heterogeneity/Half Normal
%%DATADIR%%/SubstitutionClasses/Heterogeneity/Lognormal
%%DATADIR%%/SubstitutionClasses/NucEFV/Equal
%%DATADIR%%/SubstitutionClasses/NucEFV/Estimated
%%DATADIR%%/SubstitutionClasses/NucEFV/Observed In Data Set
%%DATADIR%%/SubstitutionClasses/NucEFV/Observed In Partition
%%DATADIR%%/SubstitutionClasses/aa.bf
%%DATADIR%%/SubstitutionClasses/codon.bf
%%DATADIR%%/SubstitutionClasses/dinuc.bf
%%DATADIR%%/SubstitutionClasses/nuc.bf
%%DATADIR%%/SubstitutionModels/Aminoacid/Dayhoff.mdl
%%DATADIR%%/SubstitutionModels/Aminoacid/EIAA.mdl
%%DATADIR%%/SubstitutionModels/Aminoacid/Fitness.mdl
%%DATADIR%%/SubstitutionModels/Aminoacid/Jones.mdl
%%DATADIR%%/SubstitutionModels/Aminoacid/mtREV.mdl
%%DATADIR%%/SubstitutionModels/Binary/F81.mdl
%%DATADIR%%/SubstitutionModels/Codon/GY94_3x4.mdl
%%DATADIR%%/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94_3x4.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94_REV_3x4.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
%%DATADIR%%/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
%%DATADIR%%/SubstitutionModels/Nucleotide/EFVEstimated.ibf
%%DATADIR%%/SubstitutionModels/Nucleotide/F81.mdl
%%DATADIR%%/SubstitutionModels/Nucleotide/HKY85.mdl
%%DATADIR%%/SubstitutionModels/Nucleotide/REV.mdl
%%DATADIR%%/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
%%DATADIR%%/SubstitutionModels/Nucleotide/TrN.mdl
%%DATADIR%%/SubstitutionModels/User/Nucleotide/JC69
%%DATADIR%%/SubstitutionModels/User/Nucleotide/K2P
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/gamma1.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/gamma2.def
%%DATADIR%%/TemplateBatchFiles/AAModelComparison.bf
%%DATADIR%%/TemplateBatchFiles/AddABias.ibf
%%DATADIR%%/TemplateBatchFiles/AnalyzeCodonData.bf
%%DATADIR%%/TemplateBatchFiles/AnalyzeDiNucData.bf
%%DATADIR%%/TemplateBatchFiles/AnalyzeNucDataFreq.bf
%%DATADIR%%/TemplateBatchFiles/AnalyzeNucProtData.bf
%%DATADIR%%/TemplateBatchFiles/BGM.bf
%%DATADIR%%/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
%%DATADIR%%/TemplateBatchFiles/BranchSiteREL.bf
%%DATADIR%%/TemplateBatchFiles/BranchSiteRELMultiModel.bf
%%DATADIR%%/TemplateBatchFiles/CleanGaps.bf
%%DATADIR%%/TemplateBatchFiles/CleanStopCodons.bf
%%DATADIR%%/TemplateBatchFiles/ClusterAnalysis.bf
%%DATADIR%%/TemplateBatchFiles/ClusterByDistanceRange.bf
%%DATADIR%%/TemplateBatchFiles/CodonBivariateRateProcessor.bf
%%DATADIR%%/TemplateBatchFiles/CodonModelCompare.bf
%%DATADIR%%/TemplateBatchFiles/CodonToProtein.bf
%%DATADIR%%/TemplateBatchFiles/ConvertDataFile.bf
%%DATADIR%%/TemplateBatchFiles/DirectionalREL.bf
%%DATADIR%%/TemplateBatchFiles/DistanceMatrix.bf
%%DATADIR%%/TemplateBatchFiles/Distances/CodonTools.def
%%DATADIR%%/TemplateBatchFiles/Distances/CodonTools2.def
%%DATADIR%%/TemplateBatchFiles/Distances/CodonToolsMain.def
%%DATADIR%%/TemplateBatchFiles/Distances/JC69
%%DATADIR%%/TemplateBatchFiles/Distances/K2P
%%DATADIR%%/TemplateBatchFiles/Distances/K2P_RV
%%DATADIR%%/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
%%DATADIR%%/TemplateBatchFiles/Distances/Nei_Gojobori
%%DATADIR%%/TemplateBatchFiles/Distances/PC
%%DATADIR%%/TemplateBatchFiles/Distances/PC_MH
%%DATADIR%%/TemplateBatchFiles/Distances/PC_RV
%%DATADIR%%/TemplateBatchFiles/Distances/T3P
%%DATADIR%%/TemplateBatchFiles/Distances/TN84
%%DATADIR%%/TemplateBatchFiles/Distances/TN93
%%DATADIR%%/TemplateBatchFiles/Distances/TN93_RV
%%DATADIR%%/TemplateBatchFiles/Distances/Unaligned_LZ
%%DATADIR%%/TemplateBatchFiles/Distances/Unaligned_LZ_FR
%%DATADIR%%/TemplateBatchFiles/Distances/p_Distance
%%DATADIR%%/TemplateBatchFiles/Distances/p_Distance_aa
%%DATADIR%%/TemplateBatchFiles/Distances/p_Distance_binary
%%DATADIR%%/TemplateBatchFiles/Distances/p_Distance_codon
%%DATADIR%%/TemplateBatchFiles/F_ST.bf
%%DATADIR%%/TemplateBatchFiles/FitnessAAModels.bf
%%DATADIR%%/TemplateBatchFiles/GARD.bf
%%DATADIR%%/TemplateBatchFiles/GA_CHC.ibf
%%DATADIR%%/TemplateBatchFiles/GA_CHC_Binary.ibf
%%DATADIR%%/TemplateBatchFiles/GUI/crayolaColors.def
%%DATADIR%%/TemplateBatchFiles/Gateaux.bf
%%DATADIR%%/TemplateBatchFiles/GateauxMR.bf
%%DATADIR%%/TemplateBatchFiles/KHTest.bf
%%DATADIR%%/TemplateBatchFiles/LEISR.bf
%%DATADIR%%/TemplateBatchFiles/LHT.bf
%%DATADIR%%/TemplateBatchFiles/LRTRecombTest.bf
%%DATADIR%%/TemplateBatchFiles/LZ_Complexity.bf
%%DATADIR%%/TemplateBatchFiles/LocalMolClock.bf
%%DATADIR%%/TemplateBatchFiles/MGvsGY.bf
%%DATADIR%%/TemplateBatchFiles/MergeSequences.bf
%%DATADIR%%/TemplateBatchFiles/MergeSites.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
%%DATADIR%%/TemplateBatchFiles/ModelTest.bf
%%DATADIR%%/TemplateBatchFiles/MolClockAllRoots.bf
%%DATADIR%%/TemplateBatchFiles/MolecularClock.bf
%%DATADIR%%/TemplateBatchFiles/MSS-joint-fitter.bf
%%DATADIR%%/TemplateBatchFiles/MSS-selector-2.bf
%%DATADIR%%/TemplateBatchFiles/MSS-selector.bf
%%DATADIR%%/TemplateBatchFiles/NeighborJoining.bf
%%DATADIR%%/TemplateBatchFiles/NielsenYang.bf
%%DATADIR%%/TemplateBatchFiles/NucModelCompare.bf
%%DATADIR%%/TemplateBatchFiles/PARRIS.bf
%%DATADIR%%/TemplateBatchFiles/PairwiseRelativeRate.bf
%%DATADIR%%/TemplateBatchFiles/PairwiseRelativeRatio.bf
%%DATADIR%%/TemplateBatchFiles/PartitionDataFile.bf
%%DATADIR%%/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf
%%DATADIR%%/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf
%%DATADIR%%/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
%%DATADIR%%/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf
%%DATADIR%%/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
%%DATADIR%%/TemplateBatchFiles/ReduceDataSetMatrix.bf
%%DATADIR%%/TemplateBatchFiles/RelativeRate.bf
%%DATADIR%%/TemplateBatchFiles/RelativeRatio.bf
%%DATADIR%%/TemplateBatchFiles/SGASimProcessor.bf
%%DATADIR%%/TemplateBatchFiles/SGEmulator.bf
%%DATADIR%%/TemplateBatchFiles/SGEmulator_MF.bf
%%DATADIR%%/TemplateBatchFiles/SGIvL.bf
%%DATADIR%%/TemplateBatchFiles/SM-2019.bf
%%DATADIR%%/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf
%%DATADIR%%/TemplateBatchFiles/Samplers/lhc.bf
%%DATADIR%%/TemplateBatchFiles/Samplers/lhc_supp.ibf
%%DATADIR%%/TemplateBatchFiles/Samplers/sir.bf
%%DATADIR%%/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf
%%DATADIR%%/TemplateBatchFiles/Samplers/srs.ibf
%%DATADIR%%/TemplateBatchFiles/SandNSAmbigs.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FADE.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FEL.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/MEME.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/error-filter.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
%%DATADIR%%/TemplateBatchFiles/SelectionLRT.bf
%%DATADIR%%/TemplateBatchFiles/SeqAlignShared.ibf
%%DATADIR%%/TemplateBatchFiles/SeqAlignmentCodon.bf
%%DATADIR%%/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
%%DATADIR%%/TemplateBatchFiles/SeqAlignmentNucShared.ibf
%%DATADIR%%/TemplateBatchFiles/SequentialAddition.bf
%%DATADIR%%/TemplateBatchFiles/SequentialAddition.ibf
%%DATADIR%%/TemplateBatchFiles/SimilarityPlot.bf
%%DATADIR%%/TemplateBatchFiles/SimmondsAI.bf
%%DATADIR%%/TemplateBatchFiles/SingleBreakpointRecomb.bf
%%DATADIR%%/TemplateBatchFiles/SlidingWindowAnalysis.bf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/190
%%DATADIR%%/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/CF3x4.bf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Default
%%DATADIR%%/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/ECM+F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/ECM.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EIAA.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EX.dat
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EX.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
%%DATADIR%%/TemplateBatchFiles/TemplateModels/F81.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/F81_binary.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/F84.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/F84P.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/GRM.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/GY94.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/GY94.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/GY94w9.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/HKY85.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/JC69.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Jones.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Jones_F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/K2P.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/K3ST.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/LCAP.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MEC.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94custom.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MG94x2.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MGwAA.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/MGwEX.ibf
%%DATADIR%%/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/NRM.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/PCH
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNA16.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNA16A
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNAEqualInput
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNAF81
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNAREV
%%DATADIR%%/TemplateBatchFiles/TemplateModels/RNAREV_1
%%DATADIR%%/TemplateBatchFiles/TemplateModels/S4
%%DATADIR%%/TemplateBatchFiles/TemplateModels/STGRM.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/TrN.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/UniversalCode.def
%%DATADIR%%/TemplateBatchFiles/TemplateModels/WAG.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/WAG_F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
%%DATADIR%%/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
%%DATADIR%%/TemplateBatchFiles/TemplateModels/custm4x4.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/defineGamma.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/defineHM.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/fitness.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/modelParameters.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/models.lst
%%DATADIR%%/TemplateBatchFiles/TemplateModels/mtMAM.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/mtREV.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/reducedREV.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/rtREV.mdl
%%DATADIR%%/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
%%DATADIR%%/TemplateBatchFiles/TestBranchDNDS.bf
%%DATADIR%%/TemplateBatchFiles/TestClade.bf
%%DATADIR%%/TemplateBatchFiles/TestCladeMeans.bf
%%DATADIR%%/TemplateBatchFiles/TopologySearch.bf
%%DATADIR%%/TemplateBatchFiles/TopologySearchConstrained.bf
%%DATADIR%%/TemplateBatchFiles/TreeCorrelationCoefficients.bf
%%DATADIR%%/TemplateBatchFiles/TreeTools.ibf
%%DATADIR%%/TemplateBatchFiles/UpperBound.bf
%%DATADIR%%/TemplateBatchFiles/Utility/AncestralMapper.bf
%%DATADIR%%/TemplateBatchFiles/Utility/BranchLengthFitters.bf
%%DATADIR%%/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
%%DATADIR%%/TemplateBatchFiles/Utility/CodonTools.bf
%%DATADIR%%/TemplateBatchFiles/Utility/DBTools.ibf
%%DATADIR%%/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
%%DATADIR%%/TemplateBatchFiles/Utility/GrabBag.bf
%%DATADIR%%/TemplateBatchFiles/Utility/HXB2Mapper.bf
%%DATADIR%%/TemplateBatchFiles/Utility/LocalMGREV.bf
%%DATADIR%%/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
%%DATADIR%%/TemplateBatchFiles/Utility/MPITools.bf
%%DATADIR%%/TemplateBatchFiles/Utility/NJ.bf
%%DATADIR%%/TemplateBatchFiles/Utility/PS_Plotters.bf
%%DATADIR%%/TemplateBatchFiles/Utility/PostScript.bf
%%DATADIR%%/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
%%DATADIR%%/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
%%DATADIR%%/TemplateBatchFiles/Utility/TreeFunctions.bf
%%DATADIR%%/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
%%DATADIR%%/TemplateBatchFiles/WANC.bf
%%DATADIR%%/TemplateBatchFiles/YangNielsenBranchSite2005.bf
%%DATADIR%%/TemplateBatchFiles/_BMS_Aux.ibf
%%DATADIR%%/TemplateBatchFiles/_CMS_Aux.ibf
%%DATADIR%%/TemplateBatchFiles/_MFReader_.ibf
%%DATADIR%%/TemplateBatchFiles/_tipDater.ibf
%%DATADIR%%/TemplateBatchFiles/bayesgraph.ibf
%%DATADIR%%/TemplateBatchFiles/binomial.ibf
%%DATADIR%%/TemplateBatchFiles/branchSwappingFunctions.bf
%%DATADIR%%/TemplateBatchFiles/categoryEcho.bf
%%DATADIR%%/TemplateBatchFiles/chooseDistanceFormula.def
%%DATADIR%%/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
%%DATADIR%%/TemplateBatchFiles/dNdSDistributionComparison.bf
%%DATADIR%%/TemplateBatchFiles/dNdSRateAnalysis.bf
%%DATADIR%%/TemplateBatchFiles/dNdSResultProcessor.bf
%%DATADIR%%/TemplateBatchFiles/dSdNTreeTools.ibf
%%DATADIR%%/TemplateBatchFiles/distanceMethodNPBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/doNNISwap.bf
%%DATADIR%%/TemplateBatchFiles/doSPRSwap.bf
%%DATADIR%%/TemplateBatchFiles/files.lst
%%DATADIR%%/TemplateBatchFiles/globalChecker.ibf
%%DATADIR%%/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/last.date
%%DATADIR%%/TemplateBatchFiles/libv3/IOFunctions.bf
%%DATADIR%%/TemplateBatchFiles/libv3/UtilityFunctions.bf
%%DATADIR%%/TemplateBatchFiles/libv3/all-terms.bf
%%DATADIR%%/TemplateBatchFiles/libv3/convenience/math.bf
%%DATADIR%%/TemplateBatchFiles/libv3/convenience/matrix.bf
%%DATADIR%%/TemplateBatchFiles/libv3/convenience/random.bf
%%DATADIR%%/TemplateBatchFiles/libv3/convenience/regexp.bf
%%DATADIR%%/TemplateBatchFiles/libv3/function-loader.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/DNA.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/DNA/GTR.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/DNA/HKY85.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/DNA/JC69.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/binary.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/binary/charbinary.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/binary/empirical.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MSS.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/frequencies.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/model_functions.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/parameters.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/REV.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/empirical.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/rate_variation.bf
%%DATADIR%%/TemplateBatchFiles/libv3/stats.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/alignments.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/ancestral.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/distances.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/estimators.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/genetic_code.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/mpi.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/trees.bf
%%DATADIR%%/TemplateBatchFiles/molclockBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
%%DATADIR%%/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
%%DATADIR%%/TemplateBatchFiles/partitionSequences.ibf
%%DATADIR%%/TemplateBatchFiles/posteriors.ibf
%%DATADIR%%/TemplateBatchFiles/qndhelper1.ibf
%%DATADIR%%/TemplateBatchFiles/qndhelper1_mf.ibf
%%DATADIR%%/TemplateBatchFiles/qndhelper2.ibf
%%DATADIR%%/TemplateBatchFiles/qndhelper2_mf.ibf
%%DATADIR%%/TemplateBatchFiles/qndhelper3.ibf
%%DATADIR%%/TemplateBatchFiles/qndhelper4.ibf
%%DATADIR%%/TemplateBatchFiles/queryTree.bf
%%DATADIR%%/TemplateBatchFiles/readIndexFile.bf
%%DATADIR%%/TemplateBatchFiles/relative_nucleotide_rates.bf
%%DATADIR%%/TemplateBatchFiles/relrateBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/relratioBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/selectModelParameters.bf
%%DATADIR%%/TemplateBatchFiles/simpleBootstrap.bf
%%DATADIR%%/data/brown.nuc
%%DATADIR%%/data/integrase_BDA.nex
%%DATADIR%%/data/p51.aa
%%DATADIR%%/data/p51.nex