Package | Description |
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Alignments |
Provides class for dealing with "alignments" and the sites in an alignment.
|
Ancestors |
Provides classed to calculate ancestral reconstruction.
|
Simulations |
Provides a class to create simulate data.
|
Constructor and Description |
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Alignment(java.util.List<Site> data)
Creates an alignment
|
DuplicationAlignment(java.io.File f)
Creates a duplication alignment from a file.
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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.
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Modifier and Type | Method and Description |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction
|
Alignment |
AncestralJointBB.calculate(Parameters p) |
Alignment |
AncestralJointDP.calculate(Parameters params) |
AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction
|
Modifier and Type | Method and Description |
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Alignment |
Simulate.getAlignment(int length)
Gets a simulated alignment, not returing the state of internal nodes
|
Alignment |
Simulate.getAlignment(int length,
boolean internal)
Gets a simulated alignment
|
Alignment |
Simulate.getAlignment(int length,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment.
|
Alignment |
Simulate.getAlignment(int length,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returing the state of internal nodes.
|