Uses of Interface
pal.misc.NamedParameterized
Packages that use NamedParameterized
-
Uses of NamedParameterized in pal.substmodel
Subinterfaces of NamedParameterized in pal.substmodelModifier and TypeInterfaceDescriptioninterface
abstract base class for all rate matricesClasses in pal.substmodel that implement NamedParameterizedModifier and TypeClassDescriptionclass
abstract base class for all rate matricesclass
base class of rate matrices for amino acidsclass
BLOSUM62 model of amino acid evolutionclass
a cached rate matrix.class
base class for nucleotide rate matricesclass
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
base class for nucleotide rate matricesclass
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).