Uses of Interface
pal.substmodel.RateMatrix
Packages that use RateMatrix
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes describing substitution models, i.e.
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 RateMatrixModifier and TypeMethodDescriptionfinal 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 RateMatrixModifierConstructorDescriptionFastLikelihoodCalculator(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 RateMatrixModifier and TypeClassDescriptionclassabstract base class for all rate matricesclassbase class of rate matrices for amino acidsclassBLOSUM62 model of amino acid evolutionclassa cached rate matrix.classbase class for nucleotide rate matricesclassCPREV model of amino acid evolution (J.Adachi et al.classDayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.classFelsenstein 1981 model of nucleotide evolutionclassFelsenstein 1984 (PHYLIP) model of nucleotide evolutionclassGTR (general time reversible) model of nucleotide evolution Lanave, C., G.classHasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.classJTT model of amino acid evolution Jones, D.classMTREV24 model of amino acid evolutionclassbase class for nucleotide rate matricesclassTamura-Nei model of nucleotide evolution Tamura, K.classimplements the most general reversible rate matrix for two-state dataclassVT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.classWAG model of amino acid evolution (S.classYang'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 RateMatrixMethods in pal.substmodel that return RateMatrixModifier and TypeMethodDescriptionstatic final RateMatrixSubstitutionTool.createF81Matrix(double[] baseFrequencies) Create an F81 model of substitutionstatic final RateMatrixSubstitutionTool.createF84Matrix(double expectedTsTv, double[] baseFrequencies) Create an F84 model of substitutionstatic final RateMatrixSubstitutionTool.createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies) Create an GTR model of substitutionstatic final RateMatrixSubstitutionTool.createJC69Matrix()Create a Jukes-cantor model of substitutionstatic final RateMatrixSubstitutionTool.createTNMatrix(double kappa, double r, double[] baseFrequencies) Create an Tamura-Nei model of substitutionstatic final 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 RateMatrixModifier and TypeMethodDescriptionstatic final SubstitutionModelSubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm) static final SubstitutionModelSubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm, RateDistribution rd) static final SubstitutionModelSubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution) static final RateMatrix[]RateMatrixUtils.getCopy(RateMatrix[] toCopy) voidMatrixExponential.setMatrix(RateMatrix r) update rate matrix used in present moduleConstructors in pal.substmodel with parameters of type RateMatrixModifierConstructorDescriptionCachedRateMatrix(RateMatrix rateMatrix, int maxCacheSize) CachedRateMatrix(RateMatrix rateMatrix, DoubleKeyCache cache) create module -
Uses of RateMatrix in pal.xml
Methods in pal.xml that return RateMatrixModifier and TypeMethodDescriptionstatic RateMatrixElementParser.parseRateMatrix(Element e) Reads a rate matrix from a DOM Document element.protected static RateMatrixElementParser.parseRateMatrix(Element e, Alignment a) Reads a rate matrix from a DOM Document element.Methods in pal.xml with parameters of type RateMatrixModifier and TypeMethodDescriptionstatic ElementElementFactory.createRateMatrixElement(RateMatrix matrix, Document d)