Package pal.substmodel
Class SubstitutionTool
java.lang.Object
pal.substmodel.SubstitutionTool
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final RateMatrix
createF81Matrix
(double[] baseFrequencies) Create an F81 model of substitutionstatic final SubstitutionModel
createF81Model
(double[] baseFrequencies) Create an F81 model of substitutionstatic final RateMatrix
createF84Matrix
(double expectedTsTv, double[] baseFrequencies) Create an F84 model of substitutionstatic final SubstitutionModel
createF84Model
(double expectedTsTv, double[] baseFrequencies) Create an F84 model of substitutionstatic final RateMatrix
createGTRMatrix
(double a, double b, double c, double d, double e, double[] baseFrequencies) Create an GTR model of substitutionstatic final SubstitutionModel
createGTRModel
(double a, double b, double c, double d, double e, double[] baseFrequencies) Create an GTR model of substitutionstatic final RateMatrix
Create a Jukes-cantor model of substitutionstatic final SubstitutionModel
Create a Jukes-cantor model of substitutionstatic final SubstitutionModel
createM0YangCodonModel
(double kappa, double omega, double[] baseFrequencies) Create an base Yang Codon model (M0) of substitutionstatic final SubstitutionModel
createM1YangCodonModel
(double kappa, double p0, double[] baseFrequencies) Create an neutral Yang Codon model (M1) of substitutionstatic final SubstitutionModel
createM2YangCodonModel
(double kappa, double p0, double p1, double omega, double[] baseFrequencies) Create an Positive Yang Codon model (M2) of substitutionstatic final RateMatrix
createTNMatrix
(double kappa, double r, double[] baseFrequencies) Create an Tamura-Nei model of substitutionstatic final SubstitutionModel
createTNModel
(double kappa, double r, double[] baseFrequencies) Create an Tamura-Nei model of substitution
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Constructor Details
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SubstitutionTool
public SubstitutionTool()
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Method Details
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createJC69Model
Create a Jukes-cantor model of substitution- Returns:
- A substitution model representing JC69
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createJC69Matrix
Create a Jukes-cantor model of substitution- Returns:
- A rate matrix representing JC69
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createF81Model
Create an F81 model of substitution- Parameters:
baseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related substitution model
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createF81Matrix
Create an F81 model of substitution- Parameters:
baseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related ratematrix
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createF84Model
Create an F84 model of substitution- Parameters:
expectedTsTv
- The expected ratio of transition to transversionsbaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related substitution model
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createF84Matrix
Create an F84 model of substitution- Parameters:
expectedTsTv
- The expected ratio of transition to transversionsbaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related ratematrix
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createTNModel
public static final SubstitutionModel createTNModel(double kappa, double r, double[] baseFrequencies) Create an Tamura-Nei model of substitution- Parameters:
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiobaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related substitution model
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createTNMatrix
Create an Tamura-Nei model of substitution- Parameters:
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiobaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related ratematrix
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createGTRModel
public static final SubstitutionModel createGTRModel(double a, double b, double c, double d, double e, double[] baseFrequencies) Create an GTR model of substitution- Parameters:
a
- entry in rate matrixb
- entry in rate matrixc
- entry in rate matrixd
- entry in rate matrixe
- entry in rate matrixbaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related substitution model
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createGTRMatrix
public static final RateMatrix createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies) Create an GTR model of substitution- Parameters:
a
- entry in rate matrixb
- entry in rate matrixc
- entry in rate matrixd
- entry in rate matrixe
- entry in rate matrixbaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)- Returns:
- The related ratematrix
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createM0YangCodonModel
public static final SubstitutionModel createM0YangCodonModel(double kappa, double omega, double[] baseFrequencies) Create an base Yang Codon model (M0) of substitution- Parameters:
kappa
- transition/transversion rate ratioomega
- non-synonymous/synonymous rate ratiobaseFrequencies
- The equilibrium frequencies of the 64 codon bases (zero for stop codons please)- Returns:
- The related substitution model
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createM1YangCodonModel
public static final SubstitutionModel createM1YangCodonModel(double kappa, double p0, double[] baseFrequencies) Create an neutral Yang Codon model (M1) of substitution- Parameters:
kappa
- transition/transversion rate ratiop0
- The proporition under purifying selectionbaseFrequencies
- The equilibrium frequencies of the 64 codon bases (zero for stop codons please)- Returns:
- The related substitution model
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createM2YangCodonModel
public static final SubstitutionModel createM2YangCodonModel(double kappa, double p0, double p1, double omega, double[] baseFrequencies) Create an Positive Yang Codon model (M2) of substitution- Parameters:
kappa
- transition/transversion rate ratiop0
- The proporition under purifying selectionp1
- The proporition under neutral selectionomega
- The free omegabaseFrequencies
- The equilibrium frequencies of the 64 codon bases (zero for stop codons please)- Returns:
- The related substitution model
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