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See:
Description
Interface Summary | |
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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 | |
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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 |
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.
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