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 |
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
|