Package pal.substmodel

Classes describing substitution models, i.e. rate matrices (e.g., the HKY matrix) and rate heterogeneity distributions (e.g., the discrete Gamma distribution), as well as a class for conveniently computing transition probabilities.

See:
          Description

Interface Summary
AminoAcidModelID interface for IDs of amino acid models
NucleotideModelID interface for IDs of nucleotide models
RateMatrix abstract base class for all rate matrices
SubstitutionModel model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
 

Class Summary
AbstractRateMatrix abstract base class for all rate matrices
AminoAcidModel base class of rate matrices for amino acids
BLOSUM62 BLOSUM62 model of amino acid evolution
CachedRateMatrix a cached rate matrix.
CodonModel base class for nucleotide rate matrices
CPREV CPREV model of amino acid evolution (J.Adachi et al. 2000)
Dayhoff Dayhoff model for amino acid evolution
F81 Felsenstein 1981 model of nucleotide evolution
F84 Felsenstein 1984 (PHYLIP) model of nucleotide evolution
GammaRates discrete Gamma distribution (Z.
GTR GTR (general time reversible) model of nucleotide evolution
HKY Hasegawa-Kishino-Yano model of nucleotide evolution
InvariableSites invariable sites model (two-rate model with mean rate = 1.0)
JTT JTT model of amino acid evolution
MatrixExponential compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MTREV24 MTREV24 model of amino acid evolution
NucleotideModel base class for nucleotide rate matrices
RateDistribution abstract base class for models of rate variation over sites employing a discrete rate distribution
RateMatrixUtils  
SimpleSubstitutionModel model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
TN Tamura-Nei model of nucleotide evolution
TwoStateModel implements the most general reversible rate matrix for two-state data
UniformRate uniform rate distribution
VT VT (variable time matrix) model of amino acid evolution
WAG WAG model of amino acid evolution (S.
YangCodonModel Yang's model of codon evolution
 

Package pal.substmodel Description

Classes describing substitution models, i.e. rate matrices (e.g., the HKY matrix) and rate heterogeneity distributions (e.g., the discrete Gamma distribution), as well as a class for conveniently computing transition probabilities.