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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/DNA/
H A DHKY85.bf6 /** @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;
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/
H A DHKY85.mdl1 /* 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);
/dports/biology/hyphy/hyphy-2.5.33/Examples/ConstraintDefinition/
H A DReplicateConstraint1.bf27 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);
H A DReplicateConstraint2.bf27 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 \…
H A Dshared.bf41 /*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equ…
44 Model HKY85 = (HKY85RateMatrix , observedFreqs);
/dports/biology/py-biopython/biopython-1.79/Tests/PAML/Results/baseml/model/
H A Dmodel4-4_1.out4 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):
H A Dmodel4-4_3.out4 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):
H A Dmodel4-4_4.out4 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):
H A Dmodel4-4_4c.out4 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):
H A Dmodel4-4_5.out2 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):
H A Dmodel4-4_6.out2 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):
H A Dmodel4-4_7.out2 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):
/dports/biology/hyphy/hyphy-2.5.33/Examples/DataFilters/
H A DHKY852blocks2models.bf9 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);
H A DHKY852blocks.bf5 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
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/
H A DDNA.bf8 {"HKY85", "Hasegawa Kishino Yano 85 (HKY85) model"},
12 "HKY85": "models.DNA.HKY85.ModelDescription",
/dports/biology/paml/paml4.9j/
H A DMCbase.dat9 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
H A DMCbaseRandomTree.dat8 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
/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/libv3/
H A DLEISR.wbf38 "3": "HKY85",
45 "2": "HKY85",
/dports/biology/hyphy/hyphy-2.5.33/Examples/MoreComplexModels/
H A DExonIntron.bf11 coding regions, whereas HKY85 is used for non-coding regions.
93 /* 4 define the HKY85 model */
109 Model HKY85 = (HKY85RateMatrix, intronFreqs);
123 UseModel (HKY85);
/dports/biology/hyphy/hyphy-2.5.33/Examples/Simulation/
H A DParametricBootstrap.bf7 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. */
H A DPBootstrapHetRates.bf4 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. */
/dports/biology/hyphy/hyphy-2.5.33/Examples/SimpleAnalyses/
H A DHKY85.bf42 /*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. */
H A DHKY85shared.bf83 /*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. */
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/mrbayes/
H A DMrBayesSupport.cpp121 QString MrBayesModelTypes::HKY85("HKY85 (Nst=2)"); member in U2::MrBayesModelTypes
128 << MrBayesModelTypes::HKY85 in getSubstitutionModelTypes()
/dports/biology/hyphy/hyphy-2.5.33/Examples/SimpleConstraints/
H A DMolecularClockHKY85.bf5 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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