Index: head/biology/hyphy/Makefile =================================================================== --- head/biology/hyphy/Makefile (revision 537105) +++ head/biology/hyphy/Makefile (revision 537106) @@ -1,23 +1,23 @@ # $FreeBSD$ PORTNAME= hyphy -DISTVERSION= 2.5.12 +DISTVERSION= 2.5.14 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org COMMENT= Hypothesis testing using Phylogenies LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE ONLY_FOR_ARCHS= amd64 i386 LIB_DEPENDS= libcurl.so:ftp/curl USES= compiler:openmp cmake localbase:ldflags ssl USE_GITHUB= yes GH_ACCOUNT= veg CMAKE_ON= NOAVX .include Index: head/biology/hyphy/distinfo =================================================================== --- head/biology/hyphy/distinfo (revision 537105) +++ head/biology/hyphy/distinfo (revision 537106) @@ -1,3 +1,3 @@ -TIMESTAMP = 1588470249 -SHA256 (veg-hyphy-2.5.12_GH0.tar.gz) = ed3659371806efb6542d53ed149758a005884428fc94a27b51f897381368853f -SIZE (veg-hyphy-2.5.12_GH0.tar.gz) = 6099625 +TIMESTAMP = 1590865541 +SHA256 (veg-hyphy-2.5.14_GH0.tar.gz) = 14d2513ca5c639c160764a02f03cdd8f5e2efe2579817d3b5d9b4fbb5fe64878 +SIZE (veg-hyphy-2.5.14_GH0.tar.gz) = 6206705 Index: head/biology/hyphy/pkg-plist =================================================================== --- head/biology/hyphy/pkg-plist (revision 537105) +++ head/biology/hyphy/pkg-plist (revision 537106) @@ -1,435 +1,435 @@ bin/hyphy -lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod -lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod -lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod -lib/hyphy/GeneticCodes/Ciliate.cod -lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod -lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod -lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod -lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod -lib/hyphy/GeneticCodes/Mold_mtDNA.cod -lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod -lib/hyphy/GeneticCodes/Vertebratemtdna.cod -lib/hyphy/GeneticCodes/Yeast_mtDNA.cod -lib/hyphy/SubstitutionClasses/AAEFV/Equal -lib/hyphy/SubstitutionClasses/AAEFV/Estimated -lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set -lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition -lib/hyphy/SubstitutionClasses/CodonEFV/Equal -lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon -lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. -lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. -lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete -lib/hyphy/SubstitutionClasses/Heterogeneity/Beta -lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma -lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete -lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal -lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal -lib/hyphy/SubstitutionClasses/NucEFV/Equal -lib/hyphy/SubstitutionClasses/NucEFV/Estimated -lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set -lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition -lib/hyphy/SubstitutionClasses/aa.bf -lib/hyphy/SubstitutionClasses/codon.bf -lib/hyphy/SubstitutionClasses/dinuc.bf -lib/hyphy/SubstitutionClasses/nuc.bf -lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl -lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl -lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl -lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl -lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl -lib/hyphy/SubstitutionModels/Binary/F81.mdl -lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl -lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl -lib/hyphy/SubstitutionModels/Codon/MG94.mdl -lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl -lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl -lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl -lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl -lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl -lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl -lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl -lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl -lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf -lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl -lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl -lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl -lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl -lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl -lib/hyphy/SubstitutionModels/User/Nucleotide/JC69 -lib/hyphy/SubstitutionModels/User/Nucleotide/K2P -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def -lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def -lib/hyphy/TemplateBatchFiles/AAModelComparison.bf -lib/hyphy/TemplateBatchFiles/AddABias.ibf -lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf -lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf -lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf -lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf -lib/hyphy/TemplateBatchFiles/BGM.bf -lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf -lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf -lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf -lib/hyphy/TemplateBatchFiles/CleanGaps.bf -lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf -lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf -lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf -lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf -lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf -lib/hyphy/TemplateBatchFiles/CodonToProtein.bf -lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf -lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf -lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def -lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def -lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def -lib/hyphy/TemplateBatchFiles/Distances/JC69 -lib/hyphy/TemplateBatchFiles/Distances/K2P -lib/hyphy/TemplateBatchFiles/Distances/K2P_RV -lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori -lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori -lib/hyphy/TemplateBatchFiles/Distances/PC -lib/hyphy/TemplateBatchFiles/Distances/PC_MH -lib/hyphy/TemplateBatchFiles/Distances/PC_RV -lib/hyphy/TemplateBatchFiles/Distances/T3P -lib/hyphy/TemplateBatchFiles/Distances/TN84 -lib/hyphy/TemplateBatchFiles/Distances/TN93 -lib/hyphy/TemplateBatchFiles/Distances/TN93_RV -lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ -lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR -lib/hyphy/TemplateBatchFiles/Distances/p_Distance -lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa -lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary -lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon -lib/hyphy/TemplateBatchFiles/F_ST.bf -lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf -lib/hyphy/TemplateBatchFiles/GARD.bf -lib/hyphy/TemplateBatchFiles/GA_CHC.ibf -lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf -lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def -lib/hyphy/TemplateBatchFiles/Gateaux.bf -lib/hyphy/TemplateBatchFiles/GateauxMR.bf -lib/hyphy/TemplateBatchFiles/KHTest.bf -lib/hyphy/TemplateBatchFiles/LEISR.bf -lib/hyphy/TemplateBatchFiles/LHT.bf -lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf -lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf -lib/hyphy/TemplateBatchFiles/LocalMolClock.bf -lib/hyphy/TemplateBatchFiles/MGvsGY.bf -lib/hyphy/TemplateBatchFiles/MergeSequences.bf -lib/hyphy/TemplateBatchFiles/MergeSites.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex -lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex -lib/hyphy/TemplateBatchFiles/ModelTest.bf -lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf -lib/hyphy/TemplateBatchFiles/MolecularClock.bf -lib/hyphy/TemplateBatchFiles/NeighborJoining.bf -lib/hyphy/TemplateBatchFiles/NielsenYang.bf -lib/hyphy/TemplateBatchFiles/NucModelCompare.bf -lib/hyphy/TemplateBatchFiles/PARRIS.bf -lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf -lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf -lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf -lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf -lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf -lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md -lib/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf -lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf -lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf -lib/hyphy/TemplateBatchFiles/RelativeRate.bf -lib/hyphy/TemplateBatchFiles/RelativeRatio.bf -lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf -lib/hyphy/TemplateBatchFiles/SGEmulator.bf -lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf -lib/hyphy/TemplateBatchFiles/SGIvL.bf -lib/hyphy/TemplateBatchFiles/SM-2019.bf -lib/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf -lib/hyphy/TemplateBatchFiles/Samplers/lhc.bf -lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf -lib/hyphy/TemplateBatchFiles/Samplers/sir.bf -lib/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf -lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf -lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf -lib/hyphy/TemplateBatchFiles/SelectionLRT.bf -lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf -lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf -lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf -lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf -lib/hyphy/TemplateBatchFiles/SequentialAddition.bf -lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf -lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf -lib/hyphy/TemplateBatchFiles/SimmondsAI.bf -lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf -lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf -lib/hyphy/TemplateBatchFiles/TemplateModels/190 -lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf -lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Default -lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat -lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62 -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1 -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24 -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM -lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu -lib/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf -lib/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/PCH -lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16A -lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput -lib/hyphy/TemplateBatchFiles/TemplateModels/RNAF81 -lib/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV -lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1 -lib/hyphy/TemplateBatchFiles/TemplateModels/S4 -lib/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def -lib/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def -lib/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def -lib/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/models.lst -lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl -lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl -lib/hyphy/TemplateBatchFiles/TestBranchDNDS.bf -lib/hyphy/TemplateBatchFiles/TestClade.bf -lib/hyphy/TemplateBatchFiles/TestCladeMeans.bf -lib/hyphy/TemplateBatchFiles/TopologySearch.bf -lib/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf -lib/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf -lib/hyphy/TemplateBatchFiles/TreeTools.ibf -lib/hyphy/TemplateBatchFiles/UpperBound.bf -lib/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf -lib/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf -lib/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf -lib/hyphy/TemplateBatchFiles/Utility/CodonTools.bf -lib/hyphy/TemplateBatchFiles/Utility/DBTools.ibf -lib/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf -lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf -lib/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf -lib/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf -lib/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf -lib/hyphy/TemplateBatchFiles/Utility/MPITools.bf -lib/hyphy/TemplateBatchFiles/Utility/NJ.bf -lib/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf -lib/hyphy/TemplateBatchFiles/Utility/PostScript.bf -lib/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf -lib/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf -lib/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf -lib/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf -lib/hyphy/TemplateBatchFiles/WANC.bf -lib/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf -lib/hyphy/TemplateBatchFiles/_BMS_Aux.ibf -lib/hyphy/TemplateBatchFiles/_CMS_Aux.ibf -lib/hyphy/TemplateBatchFiles/_MFReader_.ibf -lib/hyphy/TemplateBatchFiles/_tipDater.ibf -lib/hyphy/TemplateBatchFiles/bayesgraph.ibf -lib/hyphy/TemplateBatchFiles/binomial.ibf -lib/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf -lib/hyphy/TemplateBatchFiles/categoryEcho.bf -lib/hyphy/TemplateBatchFiles/chooseDistanceFormula.def -lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf -lib/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf -lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf -lib/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf -lib/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf -lib/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf -lib/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf -lib/hyphy/TemplateBatchFiles/doNNISwap.bf -lib/hyphy/TemplateBatchFiles/doSPRSwap.bf -lib/hyphy/TemplateBatchFiles/files.lst -lib/hyphy/TemplateBatchFiles/globalChecker.ibf -lib/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf -lib/hyphy/TemplateBatchFiles/last.date -lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf -lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf -lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf -lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf -lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf -lib/hyphy/TemplateBatchFiles/libv3/convenience/random.bf -lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf -lib/hyphy/TemplateBatchFiles/libv3/function-loader.bf -lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf -lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.bf -lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf -lib/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf -lib/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf -lib/hyphy/TemplateBatchFiles/libv3/models/binary.bf -lib/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf -lib/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf -lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf -lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf -lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf -lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf -lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf -lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf -lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf -lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf -lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf -lib/hyphy/TemplateBatchFiles/libv3/models/protein.bf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf -lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf -lib/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf -lib/hyphy/TemplateBatchFiles/libv3/stats.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf -lib/hyphy/TemplateBatchFiles/libv3/tasks/distances.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf -lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf -lib/hyphy/TemplateBatchFiles/molclockBootstrap.bf -lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf -lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf -lib/hyphy/TemplateBatchFiles/partitionSequences.ibf -lib/hyphy/TemplateBatchFiles/posteriors.ibf -lib/hyphy/TemplateBatchFiles/qndhelper1.ibf -lib/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf -lib/hyphy/TemplateBatchFiles/qndhelper2.ibf -lib/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf -lib/hyphy/TemplateBatchFiles/qndhelper3.ibf -lib/hyphy/TemplateBatchFiles/qndhelper4.ibf -lib/hyphy/TemplateBatchFiles/queryTree.bf -lib/hyphy/TemplateBatchFiles/readIndexFile.bf -lib/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -lib/hyphy/TemplateBatchFiles/relrateBootstrap.bf -lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf -lib/hyphy/TemplateBatchFiles/selectModelParameters.bf -lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf -lib/hyphy/data/brown.nuc -lib/hyphy/data/integrase_BDA.nex -lib/hyphy/data/p51.aa -lib/hyphy/data/p51.nex +%%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/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/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/FUBAR.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/MEME.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/PRIME.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.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/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/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