Package pal.substmodel
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.
-
Interface Summary Interface Description AminoAcidModelID interface for IDs of amino acid modelsClassDistribution NeoRateMatrix The new RateMatrix class.NucleotideModelID interface for IDs of nucleotide modelsRateMatrix abstract base class for all rate matricesRateMatrixGroup 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 Summary Class Description AbstractRateMatrix abstract base class for all rate matricesAminoAcidModel base class of rate matrices for amino acidsBLOSUM62 BLOSUM62 model of amino acid evolutionCachedRateMatrix a cached rate matrix.CodonModel base class for nucleotide rate matricesConstantIndependentSingleSplitDistribution Title: ConstantIndependentSingleSplitDistributionCPREV 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 evolutionF84 Felsenstein 1984 (PHYLIP) model of nucleotide evolutionGammaRates 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 constraintsGTR 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 matrixMTREV24 MTREV24 model of amino acid evolutionMultiRateMatrixHandler NeutralSelectionRateMatrixGroup NucleotideModel base class for nucleotide rate matricesPositiveSelectionRateMatrixGroup RateDistribution abstract base class for models of rate variation over sites employing a discrete rate distributionRateMatrixHandler RateMatrixUtils SaturatedSingleSplitDistribution Title: SaturatedSingleSplitDistributionSequenceSimulator SimpleRateMatrixGroup SingleClassSubstitutionModel SubstitutionModel.Utils A small Utility class for things relating to Substitution Models in generalSubstitutionTool TemporalModelChange.Utils TN Tamura-Nei model of nucleotide evolution Tamura, K.TwoStateModel implements the most general reversible rate matrix for two-state dataUniformRate uniform rate distributionVariableIndependentSingleSplitDistribution Title: VariableIndependentSingleSplitDistributionVT 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