pal.substmodel
Class SubstitutionTool

java.lang.Object
  extended by 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