Uses of Interface
pal.substmodel.RateMatrix
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Packages that use RateMatrix Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.substmodel Classes describing substitution models, i.e.pal.xml Utility classes for converting PAL objects to and from XML documents. -
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Uses of RateMatrix in pal.eval
Methods in pal.eval with parameters of type RateMatrix Modifier and Type Method Description voidFastLikelihoodCalculator. setRateMatrix(RateMatrix rateMatrix)voidSimpleLikelihoodCalculator. setRateMatrix(RateMatrix m)define model (a site pattern must have been set before calling this method)Constructors in pal.eval with parameters of type RateMatrix Constructor Description FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)Constructor taking site pattern, tree and model.GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model)Constructor taking site pattern, tree and a rate matrix.GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution)Constructor taking site pattern, tree rate matrix, and a rate distributionSimpleLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model) -
Uses of RateMatrix in pal.substmodel
Classes in pal.substmodel that implement RateMatrix Modifier and Type Class Description classAbstractRateMatrixabstract base class for all rate matricesclassAminoAcidModelbase class of rate matrices for amino acidsclassBLOSUM62BLOSUM62 model of amino acid evolutionclassCachedRateMatrixa cached rate matrix.classCodonModelbase class for nucleotide rate matricesclassCPREVCPREV model of amino acid evolution (J.Adachi et al.classDayhoffDayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.classF81Felsenstein 1981 model of nucleotide evolutionclassF84Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclassGTRGTR (general time reversible) model of nucleotide evolution Lanave, C., G.classHKYHasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.classJTTJTT model of amino acid evolution Jones, D.classMTREV24MTREV24 model of amino acid evolutionclassNucleotideModelbase class for nucleotide rate matricesclassTNTamura-Nei model of nucleotide evolution Tamura, K.classTwoStateModelimplements the most general reversible rate matrix for two-state dataclassVTVT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.classWAGWAG model of amino acid evolution (S.classYangCodonModelYang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).Fields in pal.substmodel declared as RateMatrix Modifier and Type Field Description static RateMatrixF81. JC69_MATRIXMethods in pal.substmodel that return RateMatrix Modifier and Type Method Description static RateMatrixSubstitutionTool. createF81Matrix(double[] baseFrequencies)Create an F81 model of substitutionstatic RateMatrixSubstitutionTool. createF84Matrix(double expectedTsTv, double[] baseFrequencies)Create an F84 model of substitutionstatic RateMatrixSubstitutionTool. createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies)Create an GTR model of substitutionstatic RateMatrixSubstitutionTool. createJC69Matrix()Create a Jukes-cantor model of substitutionstatic RateMatrixSubstitutionTool. createTNMatrix(double kappa, double r, double[] baseFrequencies)Create an Tamura-Nei model of substitutionstatic RateMatrix[]RateMatrixUtils. getCopy(RateMatrix[] toCopy)static RateMatrixRateMatrixUtils. getInstance(int typeID, int modelID, double[] params, double[] freq)Create rate matrix given model and data type codesMethods in pal.substmodel with parameters of type RateMatrix Modifier and Type Method Description static SubstitutionModelSubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm)static SubstitutionModelSubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd)static SubstitutionModelSubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)static RateMatrix[]RateMatrixUtils. getCopy(RateMatrix[] toCopy)voidMatrixExponential. setMatrix(RateMatrix r)update rate matrix used in present moduleConstructors in pal.substmodel with parameters of type RateMatrix Constructor Description CachedRateMatrix(RateMatrix rateMatrix, int maxCacheSize)CachedRateMatrix(RateMatrix rateMatrix, DoubleKeyCache cache)MatrixExponential(RateMatrix r)create module -
Uses of RateMatrix in pal.xml
Methods in pal.xml that return RateMatrix Modifier and Type Method Description static RateMatrixElementParser. parseRateMatrix(org.w3c.dom.Element e)Reads a rate matrix from a DOM Document element.protected static RateMatrixElementParser. parseRateMatrix(org.w3c.dom.Element e, Alignment a)Reads a rate matrix from a DOM Document element.Methods in pal.xml with parameters of type RateMatrix Modifier and Type Method Description static org.w3c.dom.ElementElementFactory. createRateMatrixElement(RateMatrix matrix, org.w3c.dom.Document d)
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