Index: head/biology/hyphy/Makefile =================================================================== --- head/biology/hyphy/Makefile (revision 482494) +++ head/biology/hyphy/Makefile (revision 482495) @@ -1,21 +1,24 @@ # $FreeBSD$ PORTNAME= hyphy -DISTVERSION= 2.3.13 +DISTVERSION= 2.3.14-16 +DISTVERSIONSUFFIX= -g3d88d3e6 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:c++14-lang cmake:outsource localbase:ldflags ssl USE_GITHUB= yes GH_ACCOUNT= veg + +CMAKE_ON= NOAVX .include Index: head/biology/hyphy/distinfo =================================================================== --- head/biology/hyphy/distinfo (revision 482494) +++ head/biology/hyphy/distinfo (revision 482495) @@ -1,3 +1,3 @@ -TIMESTAMP = 1527024059 -SHA256 (veg-hyphy-2.3.13_GH0.tar.gz) = 29b72574302c98d38a92d5316b9283caa80a54c3e74c5e278c5bc9ae3d3df499 -SIZE (veg-hyphy-2.3.13_GH0.tar.gz) = 7910770 +TIMESTAMP = 1540036335 +SHA256 (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 459cd0a261ae5f31dc230847acbd294a4dc1e17fa69ef0c3db173c2b8808c826 +SIZE (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 8041349 Index: head/biology/hyphy/pkg-plist =================================================================== --- head/biology/hyphy/pkg-plist (revision 482494) +++ head/biology/hyphy/pkg-plist (revision 482495) @@ -1,593 +1,596 @@ bin/HYPHYMP lib/hyphy/ChartAddIns/Approximate_CDF lib/hyphy/ChartAddIns/Column Operations lib/hyphy/ChartAddIns/Complex Select Cells By Value lib/hyphy/ChartAddIns/Contigency Table lib/hyphy/ChartAddIns/Covariance lib/hyphy/ChartAddIns/DBAddIns/DescriptiveStats.bf lib/hyphy/ChartAddIns/DBAddIns/FromSQLFlatFile.bf lib/hyphy/ChartAddIns/DBAddIns/HY_DBW_TemplateList lib/hyphy/ChartAddIns/DBAddIns/ToChartWindow.bf lib/hyphy/ChartAddIns/DBAddIns/ToConsole.bf lib/hyphy/ChartAddIns/DBAddIns/ToFastaFile.bf lib/hyphy/ChartAddIns/DBAddIns/ToFastaFileFromPandit.bf lib/hyphy/ChartAddIns/DBAddIns/ToFrontierFastaFile.bf lib/hyphy/ChartAddIns/DBAddIns/ToSQLFlatFile.bf lib/hyphy/ChartAddIns/DBAddIns/ToTabFile.bf lib/hyphy/ChartAddIns/Descriptive Statistics lib/hyphy/ChartAddIns/Distribution Moments lib/hyphy/ChartAddIns/DistributionAddIns/Event Posteriors lib/hyphy/ChartAddIns/DistributionAddIns/Includes/posteriors.ibf lib/hyphy/ChartAddIns/DistributionAddIns/Most Likely Class Assignment lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Distribution lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Moments lib/hyphy/ChartAddIns/DistributionAddIns/Prior Moments lib/hyphy/ChartAddIns/Gaussian Penalty Clustering lib/hyphy/ChartAddIns/Goodness of Fit lib/hyphy/ChartAddIns/Histogram lib/hyphy/ChartAddIns/K-Mean Clustering lib/hyphy/ChartAddIns/KH Resampler lib/hyphy/ChartAddIns/Linear Fit lib/hyphy/ChartAddIns/Mean Profile Plot lib/hyphy/ChartAddIns/Median Profile Plot lib/hyphy/ChartAddIns/Poisson Mixture Fit lib/hyphy/ChartAddIns/Populate Cells lib/hyphy/ChartAddIns/Profile Mean Clustering lib/hyphy/ChartAddIns/Running Sum lib/hyphy/ChartAddIns/Samplers/lhc.bf lib/hyphy/ChartAddIns/Samplers/sir.bf lib/hyphy/ChartAddIns/Samplers/srs.ibf lib/hyphy/ChartAddIns/Select Cells By Index lib/hyphy/ChartAddIns/Select Cells By Value lib/hyphy/ChartAddIns/SingleColumn lib/hyphy/ChartAddIns/Sort lib/hyphy/DatapanelAddIns/Character Plot lib/hyphy/DatapanelAddIns/Character Plot Two lib/hyphy/DatapanelAddIns/Compare Subsets lib/hyphy/DatapanelAddIns/Sequence Plot lib/hyphy/DatapanelAddIns/TBD/Character Plot By Sequence lib/hyphy/DatapanelAddIns/ibfs/char_colors.def 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/454.bf lib/hyphy/TemplateBatchFiles/AAModelComparison.bf lib/hyphy/TemplateBatchFiles/AddABias.ibf lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf lib/hyphy/TemplateBatchFiles/AnalyzeCodonDataMPI.bf lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq2.bf lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData2.bf lib/hyphy/TemplateBatchFiles/BGM.bf lib/hyphy/TemplateBatchFiles/BS2007.bf lib/hyphy/TemplateBatchFiles/BUSTED-SRV.bf lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf lib/hyphy/TemplateBatchFiles/BranchClassDNDS.bf lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf lib/hyphy/TemplateBatchFiles/BranchSwap.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/CodonUsageBias.bf lib/hyphy/TemplateBatchFiles/CompareSelectivePressure.bf lib/hyphy/TemplateBatchFiles/CompareSelectivePressureIVL.bf lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf lib/hyphy/TemplateBatchFiles/DatedTipsMolecularClock.bf lib/hyphy/TemplateBatchFiles/DirectionalREL.bf lib/hyphy/TemplateBatchFiles/DirectionalREL_MF.bf lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf lib/hyphy/TemplateBatchFiles/DistanceMatrix_Splits.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/GADatedClock.bf lib/hyphy/TemplateBatchFiles/GADatedClock.ibf lib/hyphy/TemplateBatchFiles/GADatedClockProcessor.bf lib/hyphy/TemplateBatchFiles/GADatedClockProcessorM.bf lib/hyphy/TemplateBatchFiles/GARD.bf lib/hyphy/TemplateBatchFiles/GARDProcessor.bf lib/hyphy/TemplateBatchFiles/GARD_GA_CHC.ibf lib/hyphy/TemplateBatchFiles/GARecomb.bf lib/hyphy/TemplateBatchFiles/GA_CHC.ibf lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf lib/hyphy/TemplateBatchFiles/GA_CHC_kernel.ibf lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def lib/hyphy/TemplateBatchFiles/Gateaux.bf lib/hyphy/TemplateBatchFiles/Gateaux2.bf lib/hyphy/TemplateBatchFiles/GateauxMR.bf lib/hyphy/TemplateBatchFiles/KHTest.bf lib/hyphy/TemplateBatchFiles/Kernel_PCA.bf lib/hyphy/TemplateBatchFiles/Kernel_k_means.bf lib/hyphy/TemplateBatchFiles/Kernel_support.ibf lib/hyphy/TemplateBatchFiles/LEISR.bf lib/hyphy/TemplateBatchFiles/LHT.bf lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf lib/hyphy/TemplateBatchFiles/LocalBranchSiteTest.bf lib/hyphy/TemplateBatchFiles/LocalMolClock.bf lib/hyphy/TemplateBatchFiles/MEDS.bf lib/hyphy/TemplateBatchFiles/MEME_mf.bf lib/hyphy/TemplateBatchFiles/MFPSreader.def lib/hyphy/TemplateBatchFiles/MFPositiveSelection.bf lib/hyphy/TemplateBatchFiles/MFPositiveSelectionPooled.bf lib/hyphy/TemplateBatchFiles/MGvsGY.bf lib/hyphy/TemplateBatchFiles/MaxChi2.bf lib/hyphy/TemplateBatchFiles/MergeSequences.bf lib/hyphy/TemplateBatchFiles/MergeSites.bf lib/hyphy/TemplateBatchFiles/ModelSelectorAAProcessor.bf lib/hyphy/TemplateBatchFiles/ModelSelectorBranch.bf lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.bf lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.ibf lib/hyphy/TemplateBatchFiles/ModelSelectorCodonProcessor.bf lib/hyphy/TemplateBatchFiles/ModelSelectorRNA.bf lib/hyphy/TemplateBatchFiles/ModelSelectorRNA_1.bf 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/PairwiseSiteDiversity.bf lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf lib/hyphy/TemplateBatchFiles/PartitionRateComparison.bf lib/hyphy/TemplateBatchFiles/Phylohandbook.bf lib/hyphy/TemplateBatchFiles/Plato.bf lib/hyphy/TemplateBatchFiles/PositiveSelectionLI.bf lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf lib/hyphy/TemplateBatchFiles/QuickSelectionDetection-MEME-internal.bf -lib/hyphy/TemplateBatchFiles/QuickSelectionDetection.bf +lib/hyphy/TemplateBatchFiles/Deprecated/QuickSelectionDetection.bf lib/hyphy/TemplateBatchFiles/QuickSelectionDetectionMF.bf lib/hyphy/TemplateBatchFiles/RateClassCounter.bf lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf lib/hyphy/TemplateBatchFiles/RelativeRate.bf lib/hyphy/TemplateBatchFiles/RelativeRateL.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/SSRatesTest.bf lib/hyphy/TemplateBatchFiles/SampleProcessor.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.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-contrast.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.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/Simulators/BUSTED.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/FADE.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL-NS.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.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/SelectionAnalyses/testers/FitModel.bf lib/hyphy/TemplateBatchFiles/SelectionLRT.bf lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf lib/hyphy/TemplateBatchFiles/SeqAlignment.bf lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf lib/hyphy/TemplateBatchFiles/SeqAlignmentNuc.bf lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf lib/hyphy/TemplateBatchFiles/SeqAlignmentProt.bf lib/hyphy/TemplateBatchFiles/SeqAlignmentTop75.bf lib/hyphy/TemplateBatchFiles/SequentialAddition.bf lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf lib/hyphy/TemplateBatchFiles/SimmondsAI.bf lib/hyphy/TemplateBatchFiles/SimpleMutationCounter.bf lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb-2.bf lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf lib/hyphy/TemplateBatchFiles/SiteRates.bf lib/hyphy/TemplateBatchFiles/SiteRates2.bf lib/hyphy/TemplateBatchFiles/SlatkinMaddison-2parts.bf lib/hyphy/TemplateBatchFiles/SlatkinMaddison.bf lib/hyphy/TemplateBatchFiles/SlidingNucWindow.bf lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf lib/hyphy/TemplateBatchFiles/SplitSequencesByPattern.bf lib/hyphy/TemplateBatchFiles/StarDecomposition.bf lib/hyphy/TemplateBatchFiles/StrandGRMTest.bf lib/hyphy/TemplateBatchFiles/StripStopCodons.bf lib/hyphy/TemplateBatchFiles/SubtreeSelectionComparison.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/WebUpdate.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/_MSCOneStep.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/dNdSBivariateRateAnalysis_CompareDS.bf lib/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf lib/hyphy/TemplateBatchFiles/dNdSDistributionComparisonPartitions.bf lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis_MF.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/models/DNA.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/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/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/post_ancestors.bf lib/hyphy/TemplateBatchFiles/post_counting.bf lib/hyphy/TemplateBatchFiles/post_covariance.bf lib/hyphy/TemplateBatchFiles/post_dNdS.bf lib/hyphy/TemplateBatchFiles/post_lfprofile.bf lib/hyphy/TemplateBatchFiles/post_npbs.bf lib/hyphy/TemplateBatchFiles/post_pbs.bf lib/hyphy/TemplateBatchFiles/post_sampler.bf lib/hyphy/TemplateBatchFiles/post_saveResults.bf lib/hyphy/TemplateBatchFiles/post_sns.bf lib/hyphy/TemplateBatchFiles/post_variance.bf lib/hyphy/TemplateBatchFiles/post_viewResults.bf lib/hyphy/TemplateBatchFiles/postprocessors.lst 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/relrateBootstrap.bf lib/hyphy/TemplateBatchFiles/relrateBootstrapL.bf lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf lib/hyphy/TemplateBatchFiles/selectModelParameters.bf lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf lib/hyphy/TopologyInference/Exhaustive_Search lib/hyphy/TopologyInference/Neighbor_Joining lib/hyphy/TopologyInference/Sequential_Addition lib/hyphy/TopologyInference/Star_Decomposition lib/hyphy/TopologyInference/Support/branchSwappingFunctions.bf lib/hyphy/TopologyInference/Support/doNNISwap.bf lib/hyphy/TopologyInference/Support/doSPRSwap.bf lib/hyphy/TreeAddIns/Splits lib/hyphy/TreeAddIns/Tree Statistics lib/hyphy/UserAddins/AAContent lib/hyphy/UserAddins/BatchFileByURL lib/hyphy/UserAddins/BranchLengthCI lib/hyphy/UserAddins/CodonMutationToTreeMapper lib/hyphy/UserAddins/CountSubstitutions lib/hyphy/UserAddins/ExportLikelihoodFunction lib/hyphy/UserAddins/GenBankSequences lib/hyphy/UserAddins/Includes/ChooseALF.ibf lib/hyphy/UserAddins/Includes/MappersHelp.ibf lib/hyphy/UserAddins/Includes/MappersHelpAA.ibf lib/hyphy/UserAddins/LRT lib/hyphy/UserAddins/ListUserFunctions lib/hyphy/UserAddins/MapSubstitutions lib/hyphy/UserAddins/MeanPairwiseDivergence lib/hyphy/UserAddins/MeanPairwiseDivergenceSubset lib/hyphy/UserAddins/ModelCounter lib/hyphy/UserAddins/OldAddins/AAMutationCounter lib/hyphy/UserAddins/OldAddins/CodonMutationToTreeMapper.bf lib/hyphy/UserAddins/OldAddins/ColorPSTree lib/hyphy/UserAddins/OldAddins/ConvergentAndParallel lib/hyphy/UserAddins/OldAddins/CopyBranchLengths lib/hyphy/UserAddins/OldAddins/DashPSTree lib/hyphy/UserAddins/OldAddins/ExpsPerDirection lib/hyphy/UserAddins/OldAddins/FilterAssignments lib/hyphy/UserAddins/OldAddins/InferredAASubstitutionsCounter lib/hyphy/UserAddins/OldAddins/LocaldNdS lib/hyphy/UserAddins/OldAddins/ModelFitSummary lib/hyphy/UserAddins/OldAddins/ModelFitSummaryAA lib/hyphy/UserAddins/OldAddins/Multiclass DN DS inference lib/hyphy/UserAddins/OldAddins/PartitionBranchesByClasses lib/hyphy/UserAddins/OldAddins/PredictivePosteriorP lib/hyphy/UserAddins/OldAddins/RNARateMatrix lib/hyphy/UserAddins/OldAddins/SimulateAndTabDN_DS lib/hyphy/UserAddins/OldAddins/SimulateFromLF lib/hyphy/UserAddins/OldAddins/TreeLengthConstraint lib/hyphy/UserAddins/OldAddins/dNanddSTrees.bf lib/hyphy/UserAddins/OldAddins/dS and dN factors lib/hyphy/UserAddins/RecombinationProcessor.bf lib/hyphy/UserAddins/SimulateFromLF lib/hyphy/UserAddins/Tidbits lib/hyphy/data/brown.nuc lib/hyphy/data/integrase_BDA.nex lib/hyphy/data/p51.aa lib/hyphy/data/p51.nex