public final class SubstitutionTool
extends java.lang.Object
Constructor | Description |
---|---|
SubstitutionTool() |
Modifier and Type | Method | Description |
---|---|---|
static RateMatrix |
createF81Matrix(double[] baseFrequencies) |
Create an F81 model of substitution
|
static SubstitutionModel |
createF81Model(double[] baseFrequencies) |
Create an F81 model of substitution
|
static RateMatrix |
createF84Matrix(double expectedTsTv,
double[] baseFrequencies) |
Create an F84 model of substitution
|
static SubstitutionModel |
createF84Model(double expectedTsTv,
double[] baseFrequencies) |
Create an F84 model of substitution
|
static RateMatrix |
createGTRMatrix(double a,
double b,
double c,
double d,
double e,
double[] baseFrequencies) |
Create an GTR model of substitution
|
static SubstitutionModel |
createGTRModel(double a,
double b,
double c,
double d,
double e,
double[] baseFrequencies) |
Create an GTR model of substitution
|
static RateMatrix |
createJC69Matrix() |
Create a Jukes-cantor model of substitution
|
static SubstitutionModel |
createJC69Model() |
Create a Jukes-cantor model of substitution
|
static SubstitutionModel |
createM0YangCodonModel(double kappa,
double omega,
double[] baseFrequencies) |
Create an base Yang Codon model (M0) of substitution
|
static SubstitutionModel |
createM1YangCodonModel(double kappa,
double p0,
double[] baseFrequencies) |
Create an neutral Yang Codon model (M1) of substitution
|
static SubstitutionModel |
createM2YangCodonModel(double kappa,
double p0,
double p1,
double omega,
double[] baseFrequencies) |
Create an Positive Yang Codon model (M2) of substitution
|
static RateMatrix |
createTNMatrix(double kappa,
double r,
double[] baseFrequencies) |
Create an Tamura-Nei model of substitution
|
static SubstitutionModel |
createTNModel(double kappa,
double r,
double[] baseFrequencies) |
Create an Tamura-Nei model of substitution
|
public static final SubstitutionModel createJC69Model()
public static final RateMatrix createJC69Matrix()
public static final SubstitutionModel createF81Model(double[] baseFrequencies)
baseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)public static final RateMatrix createF81Matrix(double[] baseFrequencies)
baseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)public static final SubstitutionModel createF84Model(double expectedTsTv, double[] baseFrequencies)
expectedTsTv
- The expected ratio of transition to transversionsbaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)public static final RateMatrix createF84Matrix(double expectedTsTv, double[] baseFrequencies)
expectedTsTv
- The expected ratio of transition to transversionsbaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)public static final SubstitutionModel createTNModel(double kappa, double r, double[] baseFrequencies)
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiobaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)public static final RateMatrix createTNMatrix(double kappa, double r, double[] baseFrequencies)
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiobaseFrequencies
- The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)public static final SubstitutionModel createGTRModel(double a, double b, double c, double d, double e, double[] baseFrequencies)
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)public static final RateMatrix createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies)
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)public static final SubstitutionModel createM0YangCodonModel(double kappa, double omega, double[] baseFrequencies)
kappa
- transition/transversion rate ratioomega
- non-synonymous/synonymous rate ratiobaseFrequencies
- The equilibrium frequencies of the 64 codon bases (zero for stop codons please)public static final SubstitutionModel createM1YangCodonModel(double kappa, double p0, double[] baseFrequencies)
kappa
- transition/transversion rate ratiop0
- The proporition under purifying selectionbaseFrequencies
- The equilibrium frequencies of the 64 codon bases (zero for stop codons please)public static final SubstitutionModel createM2YangCodonModel(double kappa, double p0, double p1, double omega, double[] baseFrequencies)
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)