Uses of Interface
pal.misc.NamedParameterized

Packages that use NamedParameterized
pal.substmodel Classes describing substitution models, i.e. 
 

Uses of NamedParameterized in pal.substmodel
 

Subinterfaces of NamedParameterized in pal.substmodel
 interface RateMatrix
          abstract base class for all rate matrices
 

Classes in pal.substmodel that implement NamedParameterized
 class AbstractRateMatrix
          abstract base class for all rate matrices
 class AminoAcidModel
          base class of rate matrices for amino acids
 class BLOSUM62
          BLOSUM62 model of amino acid evolution
 class CachedRateMatrix
          a cached rate matrix.
 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).