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Packages that use RateMatrix | |
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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 |
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Methods in pal.eval with parameters of type RateMatrix | |
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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 | |
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FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and model. |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and a rate matrix. |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model,
RateDistribution distribution)
Constructor taking site pattern, tree rate matrix, and a rate distribution |
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SimpleLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
|
Uses of RateMatrix in pal.substmodel |
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Classes in pal.substmodel that implement RateMatrix | |
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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 | |
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static RateMatrix |
F81.JC69_MATRIX
|
Methods in pal.substmodel that return RateMatrix | |
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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 | |
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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 | |
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CachedRateMatrix(RateMatrix rateMatrix,
DoubleKeyCache cache)
|
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CachedRateMatrix(RateMatrix rateMatrix,
int maxCacheSize)
|
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MatrixExponential(RateMatrix r)
create module |
Uses of RateMatrix in pal.xml |
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Methods in pal.xml that return RateMatrix | |
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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 | |
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static org.w3c.dom.Element |
ElementFactory.createRateMatrixElement(RateMatrix matrix,
org.w3c.dom.Document d)
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