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.
|
Modifier and Type | Method and Description |
---|---|
void |
FastLikelihoodCalculator.setRateMatrix(RateMatrix rateMatrix) |
void |
SimpleLikelihoodCalculator.setRateMatrix(RateMatrix m)
define model
(a site pattern must have been set before calling this method)
|
Constructor and 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 distribution
|
SimpleLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model) |
Modifier and Type | Class and Description |
---|---|
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).
|
Modifier and Type | Field and Description |
---|---|
static RateMatrix |
F81.JC69_MATRIX |
Modifier and Type | Method and Description |
---|---|
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
|
Modifier and Type | Method and 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 module
|
Constructor and Description |
---|
CachedRateMatrix(RateMatrix rateMatrix,
DoubleKeyCache cache) |
CachedRateMatrix(RateMatrix rateMatrix,
int maxCacheSize) |
MatrixExponential(RateMatrix r)
create module
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
static org.w3c.dom.Element |
ElementFactory.createRateMatrixElement(RateMatrix matrix,
org.w3c.dom.Document d) |