Package | Description |
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Alignments |
Provides class for dealing with "alignments" and the sites in 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 | Method and Description |
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static Ambiguous |
Ambiguous.fromFile(java.io.File f)
Reads in amiguous data information from a file.
|
Constructor and Description |
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DuplicationAlignment(java.io.File f)
Creates a duplication alignment from a file.
|
DuplicationAlignment(java.io.File f,
Ambiguous ambig)
Creates a duplication alignment which contains ambiguous data.
|
SequenceAlignment(java.io.File f)
Creates a sequence alignment from a file.
|
SequenceAlignment(java.io.File f,
Ambiguous ambig)
Creates a sequence alignment from a file with ambiguouis data.
|
Modifier and Type | Method and Description |
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static Model |
Model.fromFile(java.io.File f)
Creates a new model from a file.
|
static RateCategory |
RateCategory.fromFile(java.io.File mfile)
Creates an instance from the information in a file.
|
Modifier and Type | Method and Description |
---|---|
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint) |
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint) |
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint)
Maximises the likelihood starting from a checkpoint file (see
Optimizer.setCheckPointFile(java.io.File) ,
logging to the screen. |
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint,
java.io.File log) |
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint,
java.io.File log) |
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
Maximises the likelihood starting from a checkpoint file (see
Optimizer.setCheckPointFile(java.io.File) ,
logging to a file. |
Modifier and Type | Method and Description |
---|---|
static Parameters |
Parameters.fromFile(java.io.File f)
Reads parameters from a file.
|
Modifier and Type | Method and Description |
---|---|
static Tree |
Tree.fromFile(java.io.File f)
Creates a tree from a file containing a Newick string
|