Uses of Class
pal.substmodel.AbstractRateMatrix

Packages that use AbstractRateMatrix
Package
Description
pal.substmodel
Classes describing substitution models, i.e.

  • Uses of AbstractRateMatrix in pal.substmodel

    Subclasses of AbstractRateMatrix in pal.substmodel
    Modifier and Type
    Class
    Description
    class 
    AminoAcidModel
    base class of rate matrices for amino acids
    class 
    BLOSUM62
    BLOSUM62 model of amino acid evolution
    class 
    CodonModel
    base class for nucleotide rate matrices
    class 
    CPREV
    CPREV model of amino acid evolution (J.Adachi et al.
    class 
    Dayhoff
    Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
    class 
    F81
    Felsenstein 1981 model of nucleotide evolution
    class 
    F84
    Felsenstein 1984 (PHYLIP) model of nucleotide evolution
    class 
    GTR
    GTR (general time reversible) model of nucleotide evolution Lanave, C., G.
    class 
    HKY
    Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
    class 
    JTT
    JTT model of amino acid evolution Jones, D.
    class 
    MTREV24
    MTREV24 model of amino acid evolution
    class 
    NucleotideModel
    base class for nucleotide rate matrices
    class 
    TN
    Tamura-Nei model of nucleotide evolution Tamura, K.
    class 
    TwoStateModel
    implements the most general reversible rate matrix for two-state data
    class 
    VT
    VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
    class 
    WAG
    WAG model of amino acid evolution (S.
    class 
    YangCodonModel
    Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).