Uses of Interface
pal.substmodel.RateMatrix

Packages that use RateMatrix
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. 
 

Uses of RateMatrix in pal.eval
 

Methods in pal.eval with parameters of type RateMatrix
 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
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 distribution
SimpleLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
           
 

Uses of RateMatrix in pal.substmodel
 

Classes in pal.substmodel that implement RateMatrix
 class AbstractRateMatrix
          abstract base class for all rate matrices
 class AminoAcidModel
          base class of rate matrices for amino acids
 class BLOSUM62
          BLOSUM62 model of amino acid evolution
 class CachedRateMatrix
          a cached rate matrix.
 class CodonModel
          base class for nucleotide rate matrices
 class 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 evolution
 class F84
          Felsenstein 1984 (PHYLIP) model of nucleotide evolution
 class 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 evolution
 class NucleotideModel
          base class for nucleotide rate matrices
 class TN
          Tamura-Nei model of nucleotide evolution Tamura, K.
 class TwoStateModel
          implements the most general reversible rate matrix for two-state data
 class 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
static RateMatrix F81.JC69_MATRIX
           
 

Methods in pal.substmodel that return RateMatrix
static RateMatrix SubstitutionTool.createF81Matrix(double[] baseFrequencies)
          Create an F81 model of substitution
static RateMatrix SubstitutionTool.createF84Matrix(double expectedTsTv, double[] baseFrequencies)
          Create an F84 model of substitution
static RateMatrix SubstitutionTool.createGTRMatrix(double a, double b, double c, double d, double e, double[] baseFrequencies)
          Create an GTR model of substitution
static RateMatrix SubstitutionTool.createJC69Matrix()
          Create a Jukes-cantor model of substitution
static RateMatrix SubstitutionTool.createTNMatrix(double kappa, double r, double[] baseFrequencies)
          Create an Tamura-Nei model of substitution
static 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 codes
 

Methods in pal.substmodel with parameters of type RateMatrix
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 module
 

Constructors in pal.substmodel with parameters of type RateMatrix
CachedRateMatrix(RateMatrix rateMatrix, DoubleKeyCache cache)
           
CachedRateMatrix(RateMatrix rateMatrix, int maxCacheSize)
           
MatrixExponential(RateMatrix r)
          create module
 

Uses of RateMatrix in pal.xml
 

Methods in pal.xml that return RateMatrix
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
static org.w3c.dom.Element ElementFactory.createRateMatrixElement(RateMatrix matrix, org.w3c.dom.Document d)