Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
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pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
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pal.misc |
Classes that don't fit elsewhere ;^)
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pal.substmodel |
Classes describing substitution models, i.e.
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pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Modifier and Type | Class | Description |
---|---|---|
class |
ConstantPopulation |
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
|
class |
ConstExpConst |
This class models a population that grows exponentially from an
initial population size alpha N0 at time y to a size N0
at time x until the present-day.
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class |
ConstExpGrowth |
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
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class |
DemographicClockTree |
Provides parameter interface to a clock-like genealogy which is
assumed to have some demographic pattern of theta (diversity) as
well as branch parameters (the minimal node height differences
at each internal node).
|
class |
DemographicModel |
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
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class |
ExpandingPopulation |
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
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class |
ExponentialGrowth |
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
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Modifier and Type | Method | Description |
---|---|---|
double |
LikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
|
double |
LikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Modifier and Type | Interface | Description |
---|---|---|
static interface |
DeltaModel.Instance |
Modifier and Type | Class | Description |
---|---|---|
class |
ConstantMutationRate |
This class models a constant mutation rate
(parameter: mu = mutation rate).
|
class |
MutationRateModel |
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
class |
SteppedMutationRate |
This class models a step-wise mutation rate.
|
class |
WindowedMutationRate |
This class models a windowed mutation rate
(parameter: mu = mutation rate).
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
NamedParameterized |
interface for class with (optimizable) named parameters
|
Modifier and Type | Class | Description |
---|---|---|
class |
MultiParameterized |
Title: MultiParameterized
|
static class |
Parameterized.Null |
NullParameterized Object
Can be used by subclasses to implement parameterized without actually having paramters
|
Modifier and Type | Method | Description |
---|---|---|
static Parameterized |
Parameterized.Utils.combine(Parameterized[] bases) |
Combine multiple parameterized objects into one
|
static Parameterized |
Parameterized.Utils.combine(Parameterized baseOne,
Parameterized baseTwo) |
Combine multiple parameterized objects into one
|
static Parameterized |
Parameterized.Utils.createParametizedWrapper(double[] parameters,
double[] lowerLimits,
double[] upperLimits,
double[] defaultValues) |
Create a wrapper around a set of double arrays to create a parameterized object
(changes to parameterized object change given arrays)
|
static Parameterized |
Parameterized.Utils.createParametizedWrapper(double[] parameters,
double[] lowerLimits,
double[] upperLimits,
double[] defaultValues,
double[] parametersSE) |
Create a wrapper around a set of double arrays to create a parameterized object
(changes to parameterized object change given arrays)
|
Modifier and Type | Method | Description |
---|---|---|
static Parameterized |
Parameterized.Utils.combine(Parameterized[] bases) |
Combine multiple parameterized objects into one
|
static Parameterized |
Parameterized.Utils.combine(Parameterized baseOne,
Parameterized baseTwo) |
Combine multiple parameterized objects into one
|
static MultivariateFunction |
Utils.combineMultivariateFunction(MultivariateFunction base,
Parameterized[] additionalParameters) |
Creates an interface between a parameterised object to allow it to act as
a multivariate minimum.
|
protected static int |
MultiParameterized.countParameters(Parameterized[] ps) |
|
static IndividualParameterHandler[] |
IndividualParameterHandler.Utils.createSimple(Parameterized[] bases) |
|
static IndividualParameterHandler |
IndividualParameterHandler.Utils.createSimple(Parameterized base,
int parameterIndex) |
|
static IndividualParameterHandler |
IndividualParameterHandler.Utils.createSimple(Parameterized base,
int parameterIndex,
IndividualParameterHandler.Listener listener) |
|
double[] |
MultiParameterized.getBaseParameters(Parameterized base) |
|
protected int |
MultiParameterized.getIndex(Parameterized base) |
Get the index of a base parameterized object
|
static double[] |
Parameterized.Utils.getParameters(Parameterized source) |
|
static int |
Parameterized.Utils.getTotalNumberOfParameters(Parameterized[] bases) |
|
void |
IndividualParameterHandler.Listener.parameterChanged(Parameterized base,
int parameterIndex,
double value) |
|
void |
MultiParameterized.ParameterAccessWatcher.parameterSet(Parameterized baseParameterized,
double param,
int localParameter) |
|
protected void |
Parameterized.ParameterizedUser.setParameterizedBase(Parameterized base) |
Set's the base parameterized object...
|
protected static void |
MultiParameterized.setup(Parameterized[] ps,
int[] baseLookup,
int[] baseParameter) |
|
static void |
Parameterized.Utils.setupLookups(Parameterized[] bases,
int[] baseLookup,
int[] parameterIndexLookup,
int totalNumberOfParameters) |
Constructor | Description |
---|---|
MultiParameterized(Parameterized[] bases) |
|
MultiParameterized(Parameterized[] bases,
MultiParameterized.ParameterAccessWatcher watcher) |
|
MultiParameterized(Parameterized b1,
Parameterized b2) |
|
ParameterizedNeoWrapper(Parameterized base) |
|
ParameterizedUser(Parameterized base) |
Modifier and Type | Interface | Description |
---|---|---|
interface |
RateMatrix |
abstract base class for all rate matrices
|
interface |
SubstitutionModel |
model of sequence substitution (rate matrix + rate variation).
|
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 |
CachedRateMatrix |
a cached rate matrix.
|
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 |
GammaRates |
discrete Gamma distribution (Z.
|
class |
GeneralRateDistributionSubstitutionModel |
|
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 |
InvariableSites |
invariable sites model (two-rate model with mean rate = 1.0)
|
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 |
RateDistribution |
abstract base class for models of rate variation over sites
employing a discrete rate distribution
|
class |
RateMatrixHandler |
|
class |
SingleClassSubstitutionModel |
|
class |
TN |
Tamura-Nei model of nucleotide evolution
Tamura, K.
|
class |
TwoStateModel |
implements the most general reversible rate matrix for two-state data
|
class |
UniformRate |
uniform rate distribution
|
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).
|
static class |
YangCodonModel.SimpleNeutralSelection |
A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff)
Codon model of [1] which uses the weighted sum of trwo base YangCodon models where
omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. |
static class |
YangCodonModel.SimplePositiveSelection |
A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff)
Codon model of [1] which uses the weighted sum of a three base Codon model where
omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. |
Modifier and Type | Interface | Description |
---|---|---|
interface |
ParameterizedTree |
abstract base class for a tree with an Parameterized interface
|
Modifier and Type | Class | Description |
---|---|---|
class |
ClockTree |
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node)
|
class |
LogParameterizedTree |
This class logarithmically transforms tree parameters.
|
class |
MutationRateModelTree |
Provides parameter interface to any clock-like tree with
serially sampled tips (parameters are the minimal node height differences
at each internal node).
|
static class |
ParameterizedTree.ParameterizedTreeBase |
For parameterisations that work by adjusting a base tree (that is, they aren't really
tree's themselves...)
|
class |
UnconstrainedTree |
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
|