| Interface | Description |
|---|---|
| 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 | |
| TransitionProbability |
For objects that represent a source of transition probabilities
TransitionProbability.java,v 1.3 2000/08/08 22:58:29 alexi Exp $
|
| Class | Description |
|---|---|
| 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
|