Uses of Interface
pal.util.XMLConstants
Packages that use XMLConstants
Package
Description
Classes describing substitution models, i.e.
Utility classes for converting PAL objects to and from XML documents.
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Uses of XMLConstants in pal.substmodel
Classes in pal.substmodel that implement XMLConstantsModifier and TypeClassDescriptionclass
BLOSUM62 model of amino acid evolutionclass
CPREV model of amino acid evolution (J.Adachi et al.class
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.class
Felsenstein 1981 model of nucleotide evolutionclass
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.class
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.class
JTT model of amino acid evolution Jones, D.class
MTREV24 model of amino acid evolutionclass
Tamura-Nei model of nucleotide evolution Tamura, K.class
implements the most general reversible rate matrix for two-state dataclass
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.class
WAG model of amino acid evolution (S.class
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 XMLConstantsModifier and TypeClassDescriptionclass
This class provides static methods for creating DOM Elements from PAL Objects.class
This class provides static methods for parsing PAL objects from DOM Elements.