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biology/hyphy: Update to version 2.5.4 Upstream changes: https://github.com/veg/hyphy/releases
2020-02-21 13:22:17 +01:00
bin/hyphy
biology/hyphy: Update to version 2.5.14 Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14
2020-05-30 21:39:11 +02:00
%%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
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%%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
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%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
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%%DATADIR%%/TemplateBatchFiles/2RatesAnalyses/gamma1.def
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%%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
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%%DATADIR%%/TemplateBatchFiles/Distances/Unaligned_LZ
%%DATADIR%%/TemplateBatchFiles/Distances/Unaligned_LZ_FR
%%DATADIR%%/TemplateBatchFiles/Distances/p_Distance
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%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
%%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
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%%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
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%%DATADIR%%/TemplateBatchFiles/SandNSAmbigs.bf
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%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FADE.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FEL.bf
biology/hyphy: Update to version 2.5.21
2020-10-30 15:05:47 +01:00
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
biology/hyphy: Update to version 2.5.14 Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14
2020-05-30 21:39:11 +02:00
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/MEME.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
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%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
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%%DATADIR%%/TemplateBatchFiles/SeqAlignShared.ibf
%%DATADIR%%/TemplateBatchFiles/SeqAlignmentCodon.bf
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%%DATADIR%%/TemplateBatchFiles/SimilarityPlot.bf
%%DATADIR%%/TemplateBatchFiles/SimmondsAI.bf
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%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
%%DATADIR%%/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
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%%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
Reference in a new issue Copy permalink