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Packages that use AbstractRateMatrix | |
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pal.substmodel | Classes describing substitution models, i.e. |
Uses of AbstractRateMatrix in pal.substmodel |
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Subclasses of AbstractRateMatrix in pal.substmodel | |
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class |
AminoAcidModel
base class of rate matrices for amino acids |
class |
BLOSUM62
BLOSUM62 model of amino acid evolution |
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). |
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