Package pal.substmodel

Classes describing substitution models, i.e.

See:
          Description

Interface Summary
AminoAcidModelID interface for IDs of amino acid models
ClassDistribution  
NeoRateMatrix The new RateMatrix class.
NucleotideModelID interface for IDs of nucleotide models
RateMatrix abstract base class for all rate matrices
RateMatrixGroup  
SingleSplitDistribution  
SubstitutionModel model of sequence substitution (rate matrix + rate variation).
TemporalModelChange  
 

Class Summary
AbstractRateMatrix abstract base class for all rate matrices
AminoAcidModel base class of rate matrices for amino acids
BLOSUM62 BLOSUM62 model of amino acid evolution
CachedRateMatrix a cached rate matrix.
CodonModel base class for nucleotide rate matrices
ConstantIndependentSingleSplitDistribution Title: ConstantIndependentSingleSplitDistribution
CPREV CPREV model of amino acid evolution (J.Adachi et al.
Dayhoff Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
F81 Felsenstein 1981 model of nucleotide evolution
F84 Felsenstein 1984 (PHYLIP) model of nucleotide evolution
GammaRates discrete Gamma distribution (Z.
GeneralPoissonRateMatrix A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
GeneralRateDistributionSubstitutionModel  
GeneralREVRateMatrix A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraints
GTR GTR (general time reversible) model of nucleotide evolution Lanave, C., G.
HKY Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
InvariableSites invariable sites model (two-rate model with mean rate = 1.0)
JTT JTT model of amino acid evolution Jones, D.
MatrixExponential compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MTREV24 MTREV24 model of amino acid evolution
MultiRateMatrixHandler  
NeutralSelectionRateMatrixGroup  
NucleotideModel base class for nucleotide rate matrices
PositiveSelectionRateMatrixGroup  
RateDistribution abstract base class for models of rate variation over sites employing a discrete rate distribution
RateMatrixHandler  
RateMatrixUtils  
SaturatedSingleSplitDistribution Title: SaturatedSingleSplitDistribution
SequenceSimulator  
SimpleRateMatrixGroup  
SingleClassSubstitutionModel  
SubstitutionModel.Utils A small Utility class for things relating to Substitution Models in general
SubstitutionTool  
TemporalModelChange.Utils  
TN Tamura-Nei model of nucleotide evolution Tamura, K.
TwoStateModel implements the most general reversible rate matrix for two-state data
UniformRate uniform rate distribution
VariableIndependentSingleSplitDistribution Title: VariableIndependentSingleSplitDistribution
VT VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
WAG WAG model of amino acid evolution (S.
YangCodonModel Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
YangCodonModel.SimpleNeutralSelection A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
YangCodonModel.SimplePositiveSelection A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
YangCodonModel.Utils A Utility class
 

Package pal.substmodel Description

Classes describing substitution models, i.e. rate matrices (e.g., the HKY matrix) and rate heterogeneity distributions (e.g., the discrete Gamma distribution), as well as a class for conveniently computing transition probabilities.