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 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 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)
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Uses of RateMatrix in pal.substmodel
Classes in pal.substmodel that implement RateMatrix Modifier and Type Class Description class
AbstractRateMatrix
abstract base class for all rate matricesclass
AminoAcidModel
base class of rate matrices for amino acidsclass
BLOSUM62
BLOSUM62 model of amino acid evolutionclass
CachedRateMatrix
a cached rate matrix.class
CodonModel
base class for nucleotide rate matricesclass
CPREV
CPREV model of amino acid evolution (J.Adachi et al.class
Dayhoff
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.class
F81
Felsenstein 1981 model of nucleotide evolutionclass
F84
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
GTR
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.class
HKY
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.class
JTT
JTT model of amino acid evolution Jones, D.class
MTREV24
MTREV24 model of amino acid evolutionclass
NucleotideModel
base class for nucleotide rate matricesclass
TN
Tamura-Nei model of nucleotide evolution Tamura, K.class
TwoStateModel
implements the most general reversible rate matrix for two-state dataclass
VT
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.class
WAG
WAG model of amino acid evolution (S.class
YangCodonModel
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 RateMatrix Modifier and Type Field Description static RateMatrix
F81. JC69_MATRIX
Methods in pal.substmodel that return RateMatrix Modifier and Type Method Description static RateMatrix
SubstitutionTool. createF81Matrix(double[] baseFrequencies)
Create an F81 model of substitutionstatic RateMatrix
SubstitutionTool. createF84Matrix(double expectedTsTv, double[] baseFrequencies)
Create an F84 model of substitutionstatic RateMatrix
SubstitutionTool. createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies)
Create an GTR model of substitutionstatic RateMatrix
SubstitutionTool. createJC69Matrix()
Create a Jukes-cantor model of substitutionstatic RateMatrix
SubstitutionTool. createTNMatrix(double kappa, double r, double[] baseFrequencies)
Create an Tamura-Nei model of substitutionstatic 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 RateMatrix Modifier and Type Method Description static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm)
static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd)
static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
static RateMatrix[]
RateMatrixUtils. getCopy(RateMatrix[] toCopy)
void
MatrixExponential. 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)
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Uses of RateMatrix in pal.xml
Methods in pal.xml that return RateMatrix Modifier and Type Method Description static RateMatrix
ElementParser. parseRateMatrix(org.w3c.dom.Element e)
Reads a rate matrix from a DOM Document element.protected static RateMatrix
ElementParser. 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.Element
ElementFactory. createRateMatrixElement(RateMatrix matrix, org.w3c.dom.Document d)
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