Package | Description |
---|---|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.substmodel |
Classes describing substitution models, i.e.
|
Modifier and Type | Method | Description |
---|---|---|
static ExternalParameterListener |
PalEventMulticaster.add(ExternalParameterListener old,
ExternalParameterListener toAdd) |
For managing ExternalParamterListeners
Usage: ExternalParamterListener current = null;
...
|
static ExternalParameterListener |
PalEventMulticaster.remove(ExternalParameterListener old,
ExternalParameterListener toRemove) |
For managing ExternalParamterListeners
Usage: ExternalParamterListener current = null;
...
|
Modifier and Type | Method | Description |
---|---|---|
static ExternalParameterListener |
PalEventMulticaster.add(ExternalParameterListener old,
ExternalParameterListener toAdd) |
For managing ExternalParamterListeners
Usage: ExternalParamterListener current = null;
...
|
static ExternalParameterListener |
PalEventMulticaster.remove(ExternalParameterListener old,
ExternalParameterListener toRemove) |
For managing ExternalParamterListeners
Usage: ExternalParamterListener current = null;
...
|
Modifier and Type | Class | Description |
---|---|---|
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 |
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).
|