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 void
FastLikelihoodCalculator.setRateMatrix
(RateMatrix rateMatrix) void
SimpleLikelihoodCalculator.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 TypeClassDescriptionclass
abstract base class for all rate matricesclass
base class of rate matrices for amino acidsclass
BLOSUM62 model of amino acid evolutionclass
a cached rate matrix.class
base class for nucleotide rate matricesclass
CPREV model of amino acid evolution (J.Adachi et al.class
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.class
Felsenstein 1981 model of nucleotide evolutionclass
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.class
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.class
JTT model of amino acid evolution Jones, D.class
MTREV24 model of amino acid evolutionclass
base class for nucleotide rate matricesclass
Tamura-Nei model of nucleotide evolution Tamura, K.class
implements the most general reversible rate matrix for two-state dataclass
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.class
WAG model of amino acid evolution (S.class
Yang'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 RateMatrix
SubstitutionTool.createF81Matrix
(double[] baseFrequencies) Create an F81 model of substitutionstatic final RateMatrix
SubstitutionTool.createF84Matrix
(double expectedTsTv, double[] baseFrequencies) Create an F84 model of substitutionstatic final RateMatrix
SubstitutionTool.createGTRMatrix
(double a, double b, double c, double d, double e, double[] baseFrequencies) Create an GTR model of substitutionstatic final RateMatrix
SubstitutionTool.createJC69Matrix()
Create a Jukes-cantor model of substitutionstatic final RateMatrix
SubstitutionTool.createTNMatrix
(double kappa, double r, double[] baseFrequencies) Create an Tamura-Nei model of substitutionstatic final RateMatrix[]
RateMatrixUtils.getCopy
(RateMatrix[] toCopy) static RateMatrix
RateMatrixUtils.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 SubstitutionModel
SubstitutionModel.Utils.createSubstitutionModel
(RateMatrix rm) static final SubstitutionModel
SubstitutionModel.Utils.createSubstitutionModel
(RateMatrix rm, RateDistribution rd) static final SubstitutionModel
SubstitutionModel.Utils.createSubstitutionModel
(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution) static final RateMatrix[]
RateMatrixUtils.getCopy
(RateMatrix[] toCopy) void
MatrixExponential.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 RateMatrix
ElementParser.parseRateMatrix
(Element e) Reads a rate matrix from a DOM Document element.protected static RateMatrix
ElementParser.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 Element
ElementFactory.createRateMatrixElement
(RateMatrix matrix, Document d)