Package | Description |
---|---|
Alignments |
Provides class for dealing with "alignments" and the sites in an alignment.
|
Ancestors |
Provides classed to calculate ancestral reconstruction.
|
Exceptions |
Provides exceptions that are common across the package.
|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
Models |
Provides classes for defing a phylogenetic model.
|
Optimizers |
Provides classes for optimising a likelihood.
|
Parameters |
Provides classes for defining parameters used in the various calculations.
|
Trees |
Provides classes to define a tree and any constraints on that tree.
|
Modifier and Type | Class and Description |
---|---|
class |
AlignmentException
Exception related to an alignment (currently only input errors)
|
Modifier and Type | Class and Description |
---|---|
class |
AncestralException
Exception related to ancestral reconstruction
|
Modifier and Type | Class and Description |
---|---|
class |
InputException
General excpetion for an exeption in or about an input file
|
class |
OutputException
Exception for problems writing an output file
|
Modifier and Type | Class and Description |
---|---|
static class |
Likelihood.LikelihoodException
Exception related to a likelihood calculation
|
Modifier and Type | Class and Description |
---|---|
class |
Model.ModelException
Exception thrown when there is a problem with the model
|
class |
RateCategory.RateException
Exception thrown if there is a problem within a RateClass
|
Modifier and Type | Class and Description |
---|---|
static class |
Optimizer.OptimizerException
Exception for when there is a problem with an optimiser.
|
Modifier and Type | Class and Description |
---|---|
class |
Parameters.ParameterException
Exception related to the parameters
|
Modifier and Type | Class and Description |
---|---|
class |
TreeException
Exception thrown when there is a problem with a tree
|