hyphy-common (2.5.69+dfsg-2)
Details
Core information at a glance
- Distribution
- kali
- Origin
- kali-last-snapshot
- Repository
- https://http.kali.org/kali
- Codename
- kali-last-snapshot
- Component
- main
- Source
- hyphy
- Architecture
- i386
- Section
- science
- Priority
- optional
- Maintainer
- Debian Med Packaging Team <[email protected]>
Size & integrity
Byte sizes and integrity verification
- Installed size
- 5.1 kB
- Size expected
- 611.9 kB
- Size actual
- 611.9 kB
- Size match
Dependencies
Required package dependencies
- None
Description
Hypothesis testing using Phylogenies (common files)
Tags
Package classification tags
None
Checksums
Hash values and integrity verification status
| Type | Actual | Match |
|---|---|---|
| MD5 | a8f63a91…7b73af3b | |
| SHA-1 | 6b569c0b…b3b21ed7 | |
| SHA-256 | 8dc697fe…8fd662ed | |
| SHA-512 | 995129fb…a96260b5 |
Contents
Files and directories included
. usr usr/lib usr/lib/hyphy usr/lib/hyphy/bin usr/lib/hyphy/bin/simd-dispatch usr/share usr/share/doc usr/share/doc/hyphy-common usr/share/doc/hyphy-common/changelog.Debian.gz usr/share/doc/hyphy-common/copyright usr/share/doc/hyphy-common/examples usr/share/doc/hyphy-common/examples/BatchLanguage usr/share/doc/hyphy-common/examples/BatchLanguage/MatrixIndexing.bf usr/share/doc/hyphy-common/examples/BatchLanguage/profile_test.bf usr/share/doc/hyphy-common/examples/Categories usr/share/doc/hyphy-common/examples/Categories/data usr/share/doc/hyphy-common/examples/Categories/data/aspectrin.nuc usr/share/doc/hyphy-common/examples/Categories/definitions+MLE.bf usr/share/doc/hyphy-common/examples/Categories/definitions.bf usr/share/doc/hyphy-common/examples/Categories/definitions2.bf usr/share/doc/hyphy-common/examples/Categories/definitions3.bf usr/share/doc/hyphy-common/examples/Categories/displayFunction.bf usr/share/doc/hyphy-common/examples/ConstraintDefinition usr/share/doc/hyphy-common/examples/ConstraintDefinition/ReplicateConstraint1.bf usr/share/doc/hyphy-common/examples/ConstraintDefinition/ReplicateConstraint2.bf usr/share/doc/hyphy-common/examples/ConstraintDefinition/ReplicateConstraint3.bf usr/share/doc/hyphy-common/examples/ConstraintDefinition/data usr/share/doc/hyphy-common/examples/ConstraintDefinition/data/hiv.seq usr/share/doc/hyphy-common/examples/ConstraintDefinition/shared.bf usr/share/doc/hyphy-common/examples/DataFilters usr/share/doc/hyphy-common/examples/DataFilters/HKY852blocks.bf usr/share/doc/hyphy-common/examples/DataFilters/HKY852blocks2models.bf usr/share/doc/hyphy-common/examples/DataFilters/data usr/share/doc/hyphy-common/examples/DataFilters/data/actin2.flt usr/share/doc/hyphy-common/examples/MoreComplexModels usr/share/doc/hyphy-common/examples/MoreComplexModels/ExonIntron.bf usr/share/doc/hyphy-common/examples/MoreComplexModels/Models usr/share/doc/hyphy-common/examples/MoreComplexModels/Models/EI.mdl usr/share/doc/hyphy-common/examples/MoreComplexModels/Models/MG94x2.mdl usr/share/doc/hyphy-common/examples/MoreComplexModels/aa.bf usr/share/doc/hyphy-common/examples/MoreComplexModels/data usr/share/doc/hyphy-common/examples/MoreComplexModels/data/3.seq usr/share/doc/hyphy-common/examples/MoreComplexModels/data/stewart.aa usr/share/doc/hyphy-common/examples/MoreComplexModels/data/ubiq.flt usr/share/doc/hyphy-common/examples/SimpleAnalyses usr/share/doc/hyphy-common/examples/SimpleAnalyses/F81.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/HKY85.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/HKY85shared.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/JC69.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/K2P.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/K2Pshared.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/Non-Rev.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/REV.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/REVshared.bf usr/share/doc/hyphy-common/examples/SimpleAnalyses/data usr/share/doc/hyphy-common/examples/SimpleAnalyses/data/hiv.nuc usr/share/doc/hyphy-common/examples/SimpleConstraints usr/share/doc/hyphy-common/examples/SimpleConstraints/F81K81uf_relratio.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/F81relrate.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/F81relratio.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/HKY85relrate.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/HKY85relratio.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/MolecularClockF81.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/MolecularClockHKY85.bf usr/share/doc/hyphy-common/examples/SimpleConstraints/data usr/share/doc/hyphy-common/examples/SimpleConstraints/data/3.seq usr/share/doc/hyphy-common/examples/SimpleConstraints/data/aspectrin1.nuc usr/share/doc/hyphy-common/examples/SimpleConstraints/data/aspectrin2.nuc usr/share/doc/hyphy-common/examples/SimpleConstraints/data/molclock.seq usr/share/doc/hyphy-common/examples/Simulation usr/share/doc/hyphy-common/examples/Simulation/PBootstrapHetRates.bf usr/share/doc/hyphy-common/examples/Simulation/ParametricBootstrap.bf usr/share/doc/hyphy-common/examples/Simulation/RelativeRatePBS.bf usr/share/doc/hyphy-common/examples/Simulation/data usr/share/doc/hyphy-common/examples/Simulation/data/3.seq usr/share/doc/hyphy-common/examples/Simulation/data/hiv.nuc usr/share/hyphy usr/share/hyphy/GeneticCodes usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod usr/share/hyphy/GeneticCodes/Ciliate.cod usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod usr/share/hyphy/SubstitutionClasses usr/share/hyphy/SubstitutionClasses/AAEFV usr/share/hyphy/SubstitutionClasses/AAEFV/Equal usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition usr/share/hyphy/SubstitutionClasses/CodonEFV usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. usr/share/hyphy/SubstitutionClasses/Heterogeneity usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal usr/share/hyphy/SubstitutionClasses/NucEFV usr/share/hyphy/SubstitutionClasses/NucEFV/Equal usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition usr/share/hyphy/SubstitutionClasses/aa.bf usr/share/hyphy/SubstitutionClasses/codon.bf usr/share/hyphy/SubstitutionClasses/dinuc.bf usr/share/hyphy/SubstitutionClasses/nuc.bf usr/share/hyphy/SubstitutionModels usr/share/hyphy/SubstitutionModels/Aminoacid usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl usr/share/hyphy/SubstitutionModels/Binary usr/share/hyphy/SubstitutionModels/Binary/F81.mdl usr/share/hyphy/SubstitutionModels/Codon usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl usr/share/hyphy/SubstitutionModels/Nucleotide usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl usr/share/hyphy/SubstitutionModels/User usr/share/hyphy/SubstitutionModels/User/Nucleotide usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69 usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P usr/share/hyphy/TemplateBatchFiles usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def usr/share/hyphy/TemplateBatchFiles/AAModelComparison.bf usr/share/hyphy/TemplateBatchFiles/AddABias.ibf usr/share/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf usr/share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf usr/share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf usr/share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf usr/share/hyphy/TemplateBatchFiles/BGM.bf usr/share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf usr/share/hyphy/TemplateBatchFiles/BranchSiteREL.bf usr/share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf usr/share/hyphy/TemplateBatchFiles/CleanGaps.bf usr/share/hyphy/TemplateBatchFiles/CleanStopCodons.bf usr/share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf usr/share/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf usr/share/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf usr/share/hyphy/TemplateBatchFiles/CodonModelCompare.bf usr/share/hyphy/TemplateBatchFiles/CodonToProtein.bf usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.bf usr/share/hyphy/TemplateBatchFiles/DirectionalREL.bf usr/share/hyphy/TemplateBatchFiles/DistanceMatrix.bf usr/share/hyphy/TemplateBatchFiles/Distances usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools.def usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def usr/share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def usr/share/hyphy/TemplateBatchFiles/Distances/JC69 usr/share/hyphy/TemplateBatchFiles/Distances/K2P usr/share/hyphy/TemplateBatchFiles/Distances/K2P_RV usr/share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori usr/share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori usr/share/hyphy/TemplateBatchFiles/Distances/PC usr/share/hyphy/TemplateBatchFiles/Distances/PC_MH usr/share/hyphy/TemplateBatchFiles/Distances/PC_RV usr/share/hyphy/TemplateBatchFiles/Distances/T3P usr/share/hyphy/TemplateBatchFiles/Distances/TN84 usr/share/hyphy/TemplateBatchFiles/Distances/TN93 usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_codon usr/share/hyphy/TemplateBatchFiles/F_ST.bf usr/share/hyphy/TemplateBatchFiles/FitnessAAModels.bf usr/share/hyphy/TemplateBatchFiles/GARD.bf usr/share/hyphy/TemplateBatchFiles/GA_CHC.ibf usr/share/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf usr/share/hyphy/TemplateBatchFiles/GUI usr/share/hyphy/TemplateBatchFiles/GUI/crayolaColors.def usr/share/hyphy/TemplateBatchFiles/Gateaux.bf usr/share/hyphy/TemplateBatchFiles/GateauxMR.bf usr/share/hyphy/TemplateBatchFiles/KHTest.bf usr/share/hyphy/TemplateBatchFiles/LEISR.bf usr/share/hyphy/TemplateBatchFiles/LHT.bf usr/share/hyphy/TemplateBatchFiles/LRTRecombTest.bf usr/share/hyphy/TemplateBatchFiles/LZ_Complexity.bf usr/share/hyphy/TemplateBatchFiles/LocalMolClock.bf usr/share/hyphy/TemplateBatchFiles/MGvsGY.bf usr/share/hyphy/TemplateBatchFiles/MSS-joint-fitter.bf usr/share/hyphy/TemplateBatchFiles/MSS-selector-2.bf usr/share/hyphy/TemplateBatchFiles/MSS-selector.bf usr/share/hyphy/TemplateBatchFiles/MergeSequences.bf usr/share/hyphy/TemplateBatchFiles/MergeSites.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex usr/share/hyphy/TemplateBatchFiles/ModelTest.bf usr/share/hyphy/TemplateBatchFiles/MolClockAllRoots.bf usr/share/hyphy/TemplateBatchFiles/MolecularClock.bf usr/share/hyphy/TemplateBatchFiles/NeighborJoining.bf usr/share/hyphy/TemplateBatchFiles/NielsenYang.bf usr/share/hyphy/TemplateBatchFiles/NucModelCompare.bf usr/share/hyphy/TemplateBatchFiles/PARRIS.bf usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf usr/share/hyphy/TemplateBatchFiles/PartitionDataFile.bf usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf usr/share/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf usr/share/hyphy/TemplateBatchFiles/RelativeRate.bf usr/share/hyphy/TemplateBatchFiles/RelativeRatio.bf usr/share/hyphy/TemplateBatchFiles/SGASimProcessor.bf usr/share/hyphy/TemplateBatchFiles/SGEmulator.bf usr/share/hyphy/TemplateBatchFiles/SGEmulator_MF.bf usr/share/hyphy/TemplateBatchFiles/SGIvL.bf usr/share/hyphy/TemplateBatchFiles/SM-2019.bf usr/share/hyphy/TemplateBatchFiles/Samplers usr/share/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf usr/share/hyphy/TemplateBatchFiles/Samplers/lhc.bf usr/share/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf usr/share/hyphy/TemplateBatchFiles/Samplers/sir.bf usr/share/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf 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