/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/DNA/ |
H A D | HKY85.bf | 6 /** @module models.DNA.HKY85 */ 9 * @name models.DNA.HKY85.ModelDescription 12 lfunction models.DNA.HKY85.ModelDescription(type) { 38 * @name models.DNA.HKY85.is_transition 47 * @name models.DNA.HKY85._GenerateRate 52 * @return models.DNA.HKY85._GenerateRate.p 55 models.DNA.HKY85._GenerateRate.p = {}; 69 …(models.DNA.HKY85._GenerateRate.p[model_type])[terms.parameters.transition] = models.DNA.HKY85.par… 75 models.DNA.HKY85._GenerateRate.p[terms.model.rate_entry] = models.DNA.HKY85.parameter_name; 76 return models.DNA.HKY85._GenerateRate.p; [all …]
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/ |
H A D | HKY85.mdl | 1 /* This file defines the transition matrix for the Hasegawa et al.,1985 (HKY85) 10 #Short:HKY85# 14 #FileName:HKY85.mdl# 53 HKY85 = 0; 57 MULTIPLY_BY_FREQS = PopulateModelMatrix ("HKY85",vectorOfFrequencies); 59 Model HKY85Model = (HKY85, vectorOfFrequencies, MULTIPLY_BY_FREQS);
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/dports/biology/hyphy/hyphy-2.5.33/Examples/ConstraintDefinition/ |
H A D | ReplicateConstraint1.bf | 27 fprintf (stdout, "1).Unconstrained HKY85\n\n", hivLik); 33 essentially the same as reducing the HKY85 model to the 55 fprintf (stdout, "\n\n2).HKY85 constrained to F81\n\n", hivLik); 73 fprintf (stdout, "\n\n3).HKY85 constrained to F81 on internal branches\n\n", hivLik); 78 This would be the "classic" HKY85 model, with one shared ratio. 91 fprintf (stdout, "\n\n4).HKY85 with shared ratio.\n\n", hivLik);
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H A D | ReplicateConstraint2.bf | 27 fprintf (stdout, "1).Unconstrained HKY85\n\n", hivLik); 43 fprintf (stdout, "\n\n2).HKY85 constrained to F81 on the \"iNode1\" subtree \n\n", hivLik); 55 fprintf (stdout, "\n\n3).HKY85 constrained to F81 on the \"iNode1\" branch \n\n", hivLik); 72 fprintf (stdout, "\n\n4).HKY85 with \"iNode1\" subtree constrained equal to \"iNode2\" subtree\n\n"… 87 fprintf (stdout, "\n\n5).HKY85 with \"iNode1\" subtree constrained proportional to \"iNode2\" subtr… 104 fprintf (stdout, "\n\n5).HKY85 with \"iNode1\" subtree constrained to the average of those in the \…
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H A D | shared.bf | 41 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ… 44 Model HKY85 = (HKY85RateMatrix , observedFreqs);
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/dports/biology/py-biopython/biopython-1.79/Tests/PAML/Results/baseml/model/ |
H A D | model4-4_1.out | 4 BASEML (in paml version 4.1, August 2008) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 20 Distances:HKY85 (kappa) (alpha set at 0.50) 42 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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H A D | model4-4_3.out | 4 BASEML (in paml version 4.3, August 2009) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 20 Distances:HKY85 (kappa) (alpha set at 0.50) 42 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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H A D | model4-4_4.out | 4 BASEML (in paml version 4.4, January 2010) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 20 Distances:HKY85 (kappa) (alpha set at 0.50) 42 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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H A D | model4-4_4c.out | 4 BASEML (in paml version 4.4c, August 2010) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 20 Distances:HKY85 (kappa) (alpha set at 0.50) 42 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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H A D | model4-4_5.out | 2 BASEML (in paml version 4.5, December 2011) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 18 Distances:HKY85 (kappa) (alpha set at 0.50) 40 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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H A D | model4-4_6.out | 2 BASEML (in paml version 4.6, August 2012) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 18 Distances:HKY85 (kappa) (alpha set at 0.50) 40 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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H A D | model4-4_7.out | 2 BASEML (in paml version 4.7, January 2013) Alignments/alignment.phylip HKY85 dGamma (ncatG=5) 18 Distances:HKY85 (kappa) (alpha set at 0.50) 40 Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
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/dports/biology/hyphy/hyphy-2.5.33/Examples/DataFilters/ |
H A D | HKY852blocks2models.bf | 9 and the rest. We then apply HKY85 to the 1st partition and 73 /* 4. Define the HKY85 substitution matrix. '*' is defined to be -(sum of off-diag row elements) */ 105 Model HKY85 = (HKY85RateMatrix, observedFreqs1); 119 UseModel (HKY85);
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H A D | HKY852blocks.bf | 5 applies HKY85 to both partitions. The only difference between the two 40 /* 4. Define the HKY85 substitution matrix. '*' is defined to be -(sum of off-diag row elements) */ 48 /*5. Define the HKY85 model. USE_FUNCTION_FREQUENCIES allows the model
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/ |
H A D | DNA.bf | 8 {"HKY85", "Hasegawa Kishino Yano 85 (HKY85) model"}, 12 "HKY85": "models.DNA.HKY85.ModelDescription",
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/dports/biology/paml/paml4.9j/ |
H A D | MCbase.dat | 9 7 * model: 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV 28 The kappa parameter is defined differently under HKY85 (when k=1 means 30 JC69 and F81 are considered species cases of HKY85, so use 1 for kappa
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H A D | MCbaseRandomTree.dat | 8 7 * model: 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV 28 The kappa parameter is defined differently under HKY85 (when k=1 means 30 JC69 and F81 are considered species cases of HKY85, so use 1 for kappa
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/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/libv3/ |
H A D | LEISR.wbf | 38 "3": "HKY85", 45 "2": "HKY85",
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/dports/biology/hyphy/hyphy-2.5.33/Examples/MoreComplexModels/ |
H A D | ExonIntron.bf | 11 coding regions, whereas HKY85 is used for non-coding regions. 93 /* 4 define the HKY85 model */ 109 Model HKY85 = (HKY85RateMatrix, intronFreqs); 123 UseModel (HKY85);
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/dports/biology/hyphy/hyphy-2.5.33/Examples/Simulation/ |
H A D | ParametricBootstrap.bf | 7 an HKY85 ML analysis on the data using the tree from the file. 71 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ… 77 Model HKY85 = (HKY85RateMatrix, observedFreqs); 83 and, by default, assigning the last defined model (HKY85) to all tree branches. */
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H A D | PBootstrapHetRates.bf | 4 an HKY85 with gamma rate heterogeneity ML analysis on the data using the tree from the file. 64 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ… 68 Model HKY85 = (HKY85RateMatrix, observedFreqs); 74 and, by default, assigning the last defined model (HKY85) to all tree branches. */
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/dports/biology/hyphy/hyphy-2.5.33/Examples/SimpleAnalyses/ |
H A D | HKY85.bf | 42 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ… 45 Model HKY85 = (HKY85RateMatrix, observedFreqs); 48 and, by default, assigning the last defined model (HKY85) to all tree branches. */
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H A D | HKY85shared.bf | 83 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ… 89 Model HKY85 = (HKY85RateMatrix, observedFreqs); 95 and, by default, assigning the last defined model (HKY85) to all tree branches. */
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/mrbayes/ |
H A D | MrBayesSupport.cpp | 121 QString MrBayesModelTypes::HKY85("HKY85 (Nst=2)"); member in U2::MrBayesModelTypes 128 << MrBayesModelTypes::HKY85 in getSubstitutionModelTypes()
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/dports/biology/hyphy/hyphy-2.5.33/Examples/SimpleConstraints/ |
H A D | MolecularClockHKY85.bf | 5 a series of molecular clock tests on the data using the HKY85 model. 47 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ… 50 Model HKY85 = (HKY85RateMatrix, observedFreqs);
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