Package pal.substmodel
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.
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ClassDescriptionabstract base class for all rate matricesbase class of rate matrices for amino acidsinterface for IDs of amino acid modelsBLOSUM62 model of amino acid evolutiona cached rate matrix.base class for nucleotide rate matricesTitle: ConstantIndependentSingleSplitDistributionCPREV model of amino acid evolution (J.Adachi et al.Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.Felsenstein 1981 model of nucleotide evolutionFelsenstein 1984 (PHYLIP) model of nucleotide evolutiondiscrete Gamma distribution (Z.A general rate matrix class for JC69/F81 style rate matrices (but for all data types)A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraintsGTR (general time reversible) model of nucleotide evolution Lanave, C., G.Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.invariable sites model (two-rate model with mean rate = 1.0)JTT model of amino acid evolution Jones, D.compute matrix exponential and, subsequently, transition probabilities for a given rate matrixMTREV24 model of amino acid evolutionThe new RateMatrix class.base class for nucleotide rate matricesinterface for IDs of nucleotide modelsabstract base class for models of rate variation over sites employing a discrete rate distributionabstract base class for all rate matricesTitle: SaturatedSingleSplitDistributionmodel of sequence substitution (rate matrix + rate variation).A small Utility class for things relating to Substitution Models in generalTamura-Nei model of nucleotide evolution Tamura, K.For objects that represent a source of transition probabilities TransitionProbability.java,v 1.3 2000/08/08 22:58:29 alexi Exp $implements the most general reversible rate matrix for two-state datauniform rate distributionTitle: VariableIndependentSingleSplitDistributionVT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.WAG model of amino acid evolution (S.Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).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.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.A Utility class