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Packages that use Alignment | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Ancestors | Provides classed to calculate ancestral reconstruction. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Simulations | Provides a class to create simulate data. |
Uses of Alignment in Alignments |
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Subclasses of Alignment in Alignments | |
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class |
DuplicationAlignment
Represents a duplication "alignment" - a set of gene families with their associated size in each species |
class |
FastaAlignment
Represents a sequence alignment in FASTA format |
class |
PhylipAlignment
Represents a sequence alignment in Phylip format |
class |
SequenceAlignment
Deprecated. Replaced by PhylipAlignment to allow for easier use of
multiple formats. |
Methods in Alignments that return Alignment | |
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Alignment |
Alignment.limitToTaxa(java.util.Collection<java.lang.String> limit)
Returns a new Alignment which is the same as this one except it is limited to certain taxa |
Alignment |
Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the alignment and returns it |
Alignment |
Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode,
Ambiguous ambig)
Recodes the alignment and returns it and also allows the definition of new ambiguous states |
Methods in Alignments with parameters of type Alignment | |
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static void |
DuplicationAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the duplication alignment format described above. |
static void |
FastaAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the format described in FastaAlignment.FastaAlignment(java.io.File) . |
static void |
PhylipAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the format described in PhylipAlignment.PhylipAlignment(java.io.File) . |
static void |
SequenceAlignment.writeFile(Alignment a,
java.io.File f)
Deprecated. Writes a alignment to a file in the format described in SequenceAlignment.SequenceAlignment(java.io.File) . |
Uses of Alignment in Ancestors |
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Methods in Ancestors that return Alignment | |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction |
Alignment |
AncestralJointBB.calculate(Parameters p)
|
Alignment |
AncestralJointDP.calculate(Parameters params)
|
Alignment |
AncestralMarginal.Result.getAlignment()
Gets the reconstructed alignment |
Methods in Ancestors with parameters of type Alignment | |
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static AncestralJoint |
AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
static AncestralJoint |
AncestralJoint.newInstance(Model m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
Constructors in Ancestors with parameters of type Alignment | |
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AncestralMarginal(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree. |
|
AncestralMarginal(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
java.util.Map<java.lang.String,Constrainer> con)
Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment, a tree and s et of constrainers. |
|
AncestralMarginal(Model m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree |
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AncestralMarginal(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and a constrainter |
Uses of Alignment in Likelihood |
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Constructors in Likelihood with parameters of type Alignment | |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree. |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
Alignment unobserved)
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, and unobserved data. |
|
Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
Alignment unobserved,
java.util.Map<java.lang.String,Constrainer> con)
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints. |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
java.util.Map<java.lang.String,Constrainer> con)
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints. |
|
Calculator(Model m,
Alignment a,
Tree t)
Creates an object to calculate the likelihood for a given model, alignment, tree. |
|
Calculator(Model m,
Alignment a,
Tree t,
Alignment unobserved)
Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints |
|
Calculator(Model m,
Alignment a,
Tree t,
Alignment unobserved,
Constrainer con)
Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints |
|
Calculator(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates a class to calculate the likelihood for a given model, alignment, tree and constraints |
Uses of Alignment in Simulations |
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Methods in Simulations that return Alignment | |
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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. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses)
Gets a simulated alignment, not returning the state of the internal nodes. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses,
boolean internal)
Gets a simulated alignment. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returning the state of the internal nodes. |
Methods in Simulations with parameters of type Alignment | |
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double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams)
Does a hpyothesis test on the given data and gives a p-value |
double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams,
java.util.Map<java.lang.String,java.lang.String> recode)
Does a hpyothesis test on the given data and gives a p-value |
Constructors in Simulations with parameters of type Alignment | |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given set of models, a tree, parameters and unobserved sattes. |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p,
Alignment unobserved,
java.util.Map<java.lang.String,Constrainer> con)
Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters and unobserved states. |
|
Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved,
Constrainer con)
Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints. |
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