Package pal.substmodel

Class SubstitutionTool

  • public final class SubstitutionTool
extends java.lang.Object

    • 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