Uses of Interface
pal.util.XMLConstants

Packages that use XMLConstants
Package
Description
pal.substmodel
Classes describing substitution models, i.e.
pal.xml
Utility classes for converting PAL objects to and from XML documents.

  • Uses of XMLConstants in pal.substmodel

    Classes in pal.substmodel that implement XMLConstants
    Modifier and Type
    Class
    Description
    class 
    BLOSUM62
    BLOSUM62 model of amino acid evolution
    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 
    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).

  • Uses of XMLConstants in pal.xml

    Classes in pal.xml that implement XMLConstants
    Modifier and Type
    Class
    Description
    class 
    ElementFactory
    This class provides static methods for creating DOM Elements from PAL Objects.
    class 
    ElementParser
    This class provides static methods for parsing PAL objects from DOM Elements.