Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Modifier and Type | Class | Description |
---|---|---|
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).
|
Modifier and Type | Method | Description |
---|---|---|
double[] |
ModelParameters.estimateFromTree(ParameterizedTree t) |
estimate (approximate) values for the model parameters
from the data using a given (parameterized) tree
|
static double |
LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
Optimise parameters to acheive maximum likelihood using an alternating stategy.
|
static double |
LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise parameters to acheive maximum likelihood using an alternating stategy.
|
static double |
LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
Optimise parameters to acheive maximum likelihood using a combined stategy.
|
static double |
LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise parameters to acheive maximum likelihood using a combined stategy.
|
static double |
LikelihoodOptimiser.optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
|
static double |
LikelihoodOptimiser.optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
|
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).
|
class |
UnconstrainedTree |
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
|
Modifier and Type | Method | Description |
---|---|---|
ParameterizedTree |
ParameterizedTree.Factory.generateNewTree(Tree base) |
Generate a new parameterized tree wrapped around base
|
Constructor | Description |
---|---|
LogParameterizedTree(ParameterizedTree params) |
Takes a parameterized object and transforms
the parameters logarithmically.
|