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 |
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.