Package | Description |
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pal.substmodel |
Classes describing substitution models, i.e.
|
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
Modifier and Type | Class and Description |
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class |
BLOSUM62
BLOSUM62 model of amino acid evolution
|
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 |
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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Modifier and Type | Class and Description |
---|---|
class |
ElementFactory
This class provides static methods for creating DOM Elements from PAL Objects.
|
class |
ElementParser
This class provides static methods for parsing PAL objects
from DOM Elements.
|