pal.substmodel
Class SubstitutionTool

java.lang.Object
  pal.substmodel.SubstitutionTool

public final class SubstitutionTool
extends java.lang.Object

Constructor Summary

SubstitutionTool()

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SubstitutionTool

public SubstitutionTool()

Method Detail

createJC69Model

public static final SubstitutionModel createJC69Model()

Create a Jukes-cantor model of substitution

Returns:

A substitution model representing JC69

createJC69Matrix

public static final RateMatrix createJC69Matrix()

Create a Jukes-cantor model of substitution

Returns:

A rate matrix representing JC69

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

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

createF84Model

public static final SubstitutionModel createF84Model(double expectedTsTv,
                                                     double[] baseFrequencies)

Create an F84 model of substitution

Parameters:

expectedTsTv - The expected ratio of transition to transversions

baseFrequencies - The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)

Returns:

The related substitution model

createF84Matrix

public static final RateMatrix createF84Matrix(double expectedTsTv,
                                               double[] baseFrequencies)

Create an F84 model of substitution

Parameters:

expectedTsTv - The expected ratio of transition to transversions

baseFrequencies - The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)

Returns:

The related ratematrix

createTNModel

public static final SubstitutionModel createTNModel(double kappa,
                                                    double r,
                                                    double[] baseFrequencies)

Create an Tamura-Nei model of substitution

Parameters:

kappa - transition/transversion rate ratio

r - pyrimidine/purin transition rate ratio

baseFrequencies - The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)

Returns:

The related substitution model

createTNMatrix

public static final RateMatrix createTNMatrix(double kappa,
                                              double r,
                                              double[] baseFrequencies)

Create an Tamura-Nei model of substitution

Parameters:

kappa - transition/transversion rate ratio

r - pyrimidine/purin transition rate ratio

baseFrequencies - The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)

Returns:

The related ratematrix

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 matrix

b - entry in rate matrix

c - entry in rate matrix

d - entry in rate matrix

e - entry in rate matrix

baseFrequencies - The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)

Returns:

The related substitution model

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 matrix

b - entry in rate matrix

c - entry in rate matrix

d - entry in rate matrix

e - entry in rate matrix

baseFrequencies - The equilibrium frequencies of the four nucleotide bases (ordered A, G, C, T)

Returns:

The related ratematrix

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 ratio

omega - non-synonymous/synonymous rate ratio

baseFrequencies - The equilibrium frequencies of the 64 codon bases (zero for stop codons please)

Returns:

The related substitution model

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 ratio

p0 - The proporition under purifying selection

baseFrequencies - The equilibrium frequencies of the 64 codon bases (zero for stop codons please)

Returns:

The related substitution model

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 ratio

p0 - The proporition under purifying selection

p1 - The proporition under neutral selection

omega - The free omega

baseFrequencies - The equilibrium frequencies of the 64 codon bases (zero for stop codons please)

Returns:

The related substitution model