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.