mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-24 00:45:52 +00:00
6c672c455f
This pulls in fixes after the 2.3.14 release. Upstream changes for version 2.3.14: https://github.com/veg/hyphy/releases/tag/2.3.14 Subsequent fixes: https://github.com/veg/hyphy/commit/1ecac31 https://github.com/veg/hyphy/commit/bec6833 https://github.com/veg/hyphy/commit/9847438 https://github.com/veg/hyphy/commit/02dcedd https://github.com/veg/hyphy/commit/8f44d3c https://github.com/veg/hyphy/commit/5297c30 https://github.com/veg/hyphy/commit/3d88d3e
597 lines
30 KiB
Plaintext
597 lines
30 KiB
Plaintext
bin/HYPHYMP
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lib/hyphy/ChartAddIns/Approximate_CDF
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lib/hyphy/ChartAddIns/Column Operations
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lib/hyphy/ChartAddIns/Complex Select Cells By Value
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lib/hyphy/ChartAddIns/Contigency Table
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lib/hyphy/ChartAddIns/Covariance
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lib/hyphy/ChartAddIns/DBAddIns/DescriptiveStats.bf
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lib/hyphy/ChartAddIns/DBAddIns/FromSQLFlatFile.bf
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lib/hyphy/ChartAddIns/DBAddIns/HY_DBW_TemplateList
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lib/hyphy/ChartAddIns/DBAddIns/ToChartWindow.bf
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lib/hyphy/ChartAddIns/DBAddIns/ToConsole.bf
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lib/hyphy/ChartAddIns/DBAddIns/ToFastaFile.bf
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lib/hyphy/ChartAddIns/DBAddIns/ToFastaFileFromPandit.bf
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lib/hyphy/ChartAddIns/DBAddIns/ToFrontierFastaFile.bf
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lib/hyphy/ChartAddIns/DBAddIns/ToSQLFlatFile.bf
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lib/hyphy/ChartAddIns/DBAddIns/ToTabFile.bf
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lib/hyphy/ChartAddIns/Descriptive Statistics
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lib/hyphy/ChartAddIns/Distribution Moments
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lib/hyphy/ChartAddIns/DistributionAddIns/Event Posteriors
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lib/hyphy/ChartAddIns/DistributionAddIns/Includes/posteriors.ibf
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lib/hyphy/ChartAddIns/DistributionAddIns/Most Likely Class Assignment
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lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Distribution
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lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Moments
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lib/hyphy/ChartAddIns/DistributionAddIns/Prior Moments
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lib/hyphy/ChartAddIns/Gaussian Penalty Clustering
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lib/hyphy/ChartAddIns/Goodness of Fit
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lib/hyphy/ChartAddIns/Histogram
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lib/hyphy/ChartAddIns/K-Mean Clustering
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lib/hyphy/ChartAddIns/KH Resampler
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lib/hyphy/ChartAddIns/Linear Fit
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lib/hyphy/ChartAddIns/Mean Profile Plot
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lib/hyphy/ChartAddIns/Median Profile Plot
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lib/hyphy/ChartAddIns/Poisson Mixture Fit
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lib/hyphy/ChartAddIns/Populate Cells
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lib/hyphy/ChartAddIns/Profile Mean Clustering
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lib/hyphy/ChartAddIns/Running Sum
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lib/hyphy/ChartAddIns/Samplers/lhc.bf
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lib/hyphy/ChartAddIns/Samplers/sir.bf
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lib/hyphy/ChartAddIns/Samplers/srs.ibf
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lib/hyphy/ChartAddIns/Select Cells By Index
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lib/hyphy/ChartAddIns/Select Cells By Value
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lib/hyphy/ChartAddIns/SingleColumn
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lib/hyphy/ChartAddIns/Sort
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lib/hyphy/DatapanelAddIns/Character Plot
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lib/hyphy/DatapanelAddIns/Character Plot Two
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lib/hyphy/DatapanelAddIns/Compare Subsets
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lib/hyphy/DatapanelAddIns/Sequence Plot
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lib/hyphy/DatapanelAddIns/TBD/Character Plot By Sequence
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lib/hyphy/DatapanelAddIns/ibfs/char_colors.def
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lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
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lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod
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lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
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lib/hyphy/GeneticCodes/Ciliate.cod
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lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
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lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod
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lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod
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lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
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lib/hyphy/GeneticCodes/Mold_mtDNA.cod
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lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
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lib/hyphy/GeneticCodes/Vertebratemtdna.cod
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lib/hyphy/GeneticCodes/Yeast_mtDNA.cod
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lib/hyphy/SubstitutionClasses/AAEFV/Equal
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lib/hyphy/SubstitutionClasses/AAEFV/Estimated
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lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
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lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
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lib/hyphy/SubstitutionClasses/CodonEFV/Equal
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lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
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lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
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lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
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lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
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lib/hyphy/SubstitutionClasses/Heterogeneity/Beta
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lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
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lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
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lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
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lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
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lib/hyphy/SubstitutionClasses/NucEFV/Equal
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lib/hyphy/SubstitutionClasses/NucEFV/Estimated
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lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
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lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
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lib/hyphy/SubstitutionClasses/aa.bf
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lib/hyphy/SubstitutionClasses/codon.bf
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lib/hyphy/SubstitutionClasses/dinuc.bf
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lib/hyphy/SubstitutionClasses/nuc.bf
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lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
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lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
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lib/hyphy/SubstitutionModels/Binary/F81.mdl
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lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
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lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
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lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
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lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
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lib/hyphy/SubstitutionModels/User/Nucleotide/JC69
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lib/hyphy/SubstitutionModels/User/Nucleotide/K2P
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
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lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
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lib/hyphy/TemplateBatchFiles/454.bf
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lib/hyphy/TemplateBatchFiles/AAModelComparison.bf
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lib/hyphy/TemplateBatchFiles/AddABias.ibf
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lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeCodonDataMPI.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq2.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
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lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData2.bf
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lib/hyphy/TemplateBatchFiles/BGM.bf
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lib/hyphy/TemplateBatchFiles/BS2007.bf
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lib/hyphy/TemplateBatchFiles/BUSTED-SRV.bf
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lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
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lib/hyphy/TemplateBatchFiles/BranchClassDNDS.bf
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lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf
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lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
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lib/hyphy/TemplateBatchFiles/BranchSwap.bf
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lib/hyphy/TemplateBatchFiles/CleanGaps.bf
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lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf
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lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
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lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
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lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
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lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf
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lib/hyphy/TemplateBatchFiles/CodonToProtein.bf
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lib/hyphy/TemplateBatchFiles/CodonUsageBias.bf
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lib/hyphy/TemplateBatchFiles/CompareSelectivePressure.bf
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lib/hyphy/TemplateBatchFiles/CompareSelectivePressureIVL.bf
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lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf
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lib/hyphy/TemplateBatchFiles/DatedTipsMolecularClock.bf
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lib/hyphy/TemplateBatchFiles/DirectionalREL.bf
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lib/hyphy/TemplateBatchFiles/DirectionalREL_MF.bf
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lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf
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lib/hyphy/TemplateBatchFiles/DistanceMatrix_Splits.bf
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lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def
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lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
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lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
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lib/hyphy/TemplateBatchFiles/Distances/JC69
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lib/hyphy/TemplateBatchFiles/Distances/K2P
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lib/hyphy/TemplateBatchFiles/Distances/K2P_RV
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lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
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lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
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lib/hyphy/TemplateBatchFiles/Distances/PC
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lib/hyphy/TemplateBatchFiles/Distances/PC_MH
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lib/hyphy/TemplateBatchFiles/Distances/PC_RV
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lib/hyphy/TemplateBatchFiles/Distances/T3P
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lib/hyphy/TemplateBatchFiles/Distances/TN84
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lib/hyphy/TemplateBatchFiles/Distances/TN93
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lib/hyphy/TemplateBatchFiles/Distances/TN93_RV
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lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
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lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
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lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
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lib/hyphy/TemplateBatchFiles/F_ST.bf
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lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf
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lib/hyphy/TemplateBatchFiles/GADatedClock.bf
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lib/hyphy/TemplateBatchFiles/GADatedClock.ibf
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lib/hyphy/TemplateBatchFiles/GADatedClockProcessor.bf
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lib/hyphy/TemplateBatchFiles/GADatedClockProcessorM.bf
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lib/hyphy/TemplateBatchFiles/GARD.bf
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lib/hyphy/TemplateBatchFiles/GARDProcessor.bf
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lib/hyphy/TemplateBatchFiles/GARD_GA_CHC.ibf
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lib/hyphy/TemplateBatchFiles/GARecomb.bf
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lib/hyphy/TemplateBatchFiles/GA_CHC.ibf
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lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
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lib/hyphy/TemplateBatchFiles/GA_CHC_kernel.ibf
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lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
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lib/hyphy/TemplateBatchFiles/Gateaux.bf
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lib/hyphy/TemplateBatchFiles/Gateaux2.bf
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lib/hyphy/TemplateBatchFiles/GateauxMR.bf
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lib/hyphy/TemplateBatchFiles/KHTest.bf
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lib/hyphy/TemplateBatchFiles/Kernel_PCA.bf
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lib/hyphy/TemplateBatchFiles/Kernel_k_means.bf
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lib/hyphy/TemplateBatchFiles/Kernel_support.ibf
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lib/hyphy/TemplateBatchFiles/LEISR.bf
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lib/hyphy/TemplateBatchFiles/LHT.bf
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lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf
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lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf
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lib/hyphy/TemplateBatchFiles/LocalBranchSiteTest.bf
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lib/hyphy/TemplateBatchFiles/LocalMolClock.bf
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lib/hyphy/TemplateBatchFiles/MEDS.bf
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lib/hyphy/TemplateBatchFiles/MEME_mf.bf
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lib/hyphy/TemplateBatchFiles/MFPSreader.def
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lib/hyphy/TemplateBatchFiles/MFPositiveSelection.bf
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lib/hyphy/TemplateBatchFiles/MFPositiveSelectionPooled.bf
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lib/hyphy/TemplateBatchFiles/MGvsGY.bf
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lib/hyphy/TemplateBatchFiles/MaxChi2.bf
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lib/hyphy/TemplateBatchFiles/MergeSequences.bf
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lib/hyphy/TemplateBatchFiles/MergeSites.bf
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lib/hyphy/TemplateBatchFiles/ModelSelectorAAProcessor.bf
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lib/hyphy/TemplateBatchFiles/ModelSelectorBranch.bf
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lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.bf
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lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.ibf
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lib/hyphy/TemplateBatchFiles/ModelSelectorCodonProcessor.bf
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lib/hyphy/TemplateBatchFiles/ModelSelectorRNA.bf
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lib/hyphy/TemplateBatchFiles/ModelSelectorRNA_1.bf
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lib/hyphy/TemplateBatchFiles/ModelTest.bf
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lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
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lib/hyphy/TemplateBatchFiles/MolecularClock.bf
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lib/hyphy/TemplateBatchFiles/NeighborJoining.bf
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lib/hyphy/TemplateBatchFiles/NielsenYang.bf
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lib/hyphy/TemplateBatchFiles/NucModelCompare.bf
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lib/hyphy/TemplateBatchFiles/PARRIS.bf
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lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
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lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
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lib/hyphy/TemplateBatchFiles/PairwiseSiteDiversity.bf
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lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf
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lib/hyphy/TemplateBatchFiles/PartitionRateComparison.bf
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lib/hyphy/TemplateBatchFiles/Phylohandbook.bf
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lib/hyphy/TemplateBatchFiles/Plato.bf
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lib/hyphy/TemplateBatchFiles/PositiveSelectionLI.bf
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
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lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
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lib/hyphy/TemplateBatchFiles/QuickSelectionDetection-MEME-internal.bf
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lib/hyphy/TemplateBatchFiles/Deprecated/QuickSelectionDetection.bf
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lib/hyphy/TemplateBatchFiles/QuickSelectionDetectionMF.bf
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lib/hyphy/TemplateBatchFiles/RateClassCounter.bf
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lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
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lib/hyphy/TemplateBatchFiles/RelativeRate.bf
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lib/hyphy/TemplateBatchFiles/RelativeRateL.bf
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lib/hyphy/TemplateBatchFiles/RelativeRatio.bf
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lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf
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lib/hyphy/TemplateBatchFiles/SGEmulator.bf
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lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
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lib/hyphy/TemplateBatchFiles/SGIvL.bf
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lib/hyphy/TemplateBatchFiles/SSRatesTest.bf
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lib/hyphy/TemplateBatchFiles/SampleProcessor.bf
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lib/hyphy/TemplateBatchFiles/Samplers/lhc.bf
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lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
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lib/hyphy/TemplateBatchFiles/Samplers/sir.bf
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lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf
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lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-contrast.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/BUSTED.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/FADE.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL-NS.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
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lib/hyphy/TemplateBatchFiles/SelectionAnalyses/testers/FitModel.bf
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lib/hyphy/TemplateBatchFiles/SelectionLRT.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
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lib/hyphy/TemplateBatchFiles/SeqAlignment.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentNuc.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentProt.bf
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lib/hyphy/TemplateBatchFiles/SeqAlignmentTop75.bf
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lib/hyphy/TemplateBatchFiles/SequentialAddition.bf
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lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf
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lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf
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lib/hyphy/TemplateBatchFiles/SimmondsAI.bf
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lib/hyphy/TemplateBatchFiles/SimpleMutationCounter.bf
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lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb-2.bf
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lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
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lib/hyphy/TemplateBatchFiles/SiteRates.bf
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lib/hyphy/TemplateBatchFiles/SiteRates2.bf
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lib/hyphy/TemplateBatchFiles/SlatkinMaddison-2parts.bf
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lib/hyphy/TemplateBatchFiles/SlatkinMaddison.bf
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lib/hyphy/TemplateBatchFiles/SlidingNucWindow.bf
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lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
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lib/hyphy/TemplateBatchFiles/SplitSequencesByPattern.bf
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lib/hyphy/TemplateBatchFiles/StarDecomposition.bf
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lib/hyphy/TemplateBatchFiles/StrandGRMTest.bf
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lib/hyphy/TemplateBatchFiles/StripStopCodons.bf
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lib/hyphy/TemplateBatchFiles/SubtreeSelectionComparison.bf
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lib/hyphy/TemplateBatchFiles/TemplateModels/190
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lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
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lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/Default
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
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lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
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