Package pal.substmodel

Class SubstitutionTool

java.lang.Object
pal.substmodel.SubstitutionTool
public final class SubstitutionTool extends Object

  • Constructor Details

    • SubstitutionTool

      public SubstitutionTool()

  • Method Details

    • 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