Package pal.substmodel
Class SubstitutionTool
- java.lang.Object
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- pal.substmodel.SubstitutionTool
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public final class SubstitutionTool extends java.lang.Object
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Constructor Summary
Constructors Constructor Description SubstitutionTool()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static RateMatrix
createF81Matrix(double[] baseFrequencies)
Create an F81 model of substitutionstatic SubstitutionModel
createF81Model(double[] baseFrequencies)
Create an F81 model of substitutionstatic RateMatrix
createF84Matrix(double expectedTsTv, double[] baseFrequencies)
Create an F84 model of substitutionstatic SubstitutionModel
createF84Model(double expectedTsTv, double[] baseFrequencies)
Create an F84 model of substitutionstatic RateMatrix
createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies)
Create an GTR model of substitutionstatic SubstitutionModel
createGTRModel(double a, double b, double c, double d, double e, double[] baseFrequencies)
Create an GTR model of substitutionstatic RateMatrix
createJC69Matrix()
Create a Jukes-cantor model of substitutionstatic SubstitutionModel
createJC69Model()
Create a Jukes-cantor model of substitutionstatic SubstitutionModel
createM0YangCodonModel(double kappa, double omega, double[] baseFrequencies)
Create an base Yang Codon model (M0) of substitutionstatic SubstitutionModel
createM1YangCodonModel(double kappa, double p0, double[] baseFrequencies)
Create an neutral Yang Codon model (M1) of substitutionstatic SubstitutionModel
createM2YangCodonModel(double kappa, double p0, double p1, double omega, double[] baseFrequencies)
Create an Positive Yang Codon model (M2) of substitutionstatic RateMatrix
createTNMatrix(double kappa, double r, double[] baseFrequencies)
Create an Tamura-Nei model of substitutionstatic SubstitutionModel
createTNModel(double kappa, double r, double[] baseFrequencies)
Create an Tamura-Nei model of substitution
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Method Detail
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createJC69Model
public static final SubstitutionModel createJC69Model()
Create a Jukes-cantor model of substitution- Returns:
- A substitution model representing JC69
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createJC69Matrix
public static final RateMatrix createJC69Matrix()
Create a Jukes-cantor model of substitution- Returns:
- A rate matrix representing JC69
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createF81Model
public static final SubstitutionModel createF81Model(double[] baseFrequencies)
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
public static final RateMatrix createF81Matrix(double[] baseFrequencies)
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
public static final SubstitutionModel createF84Model(double expectedTsTv, double[] baseFrequencies)
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
public static final RateMatrix createF84Matrix(double expectedTsTv, double[] baseFrequencies)
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
public static final RateMatrix createTNMatrix(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 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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