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Packages that use Trees | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Ancestors | Provides classed to calculate ancestral reconstruction. |
Constraints | Provides classes to constrain the state of internal nodes. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Optimizers | Provides classes for optimising a likelihood. |
Simulations | Provides a class to create simulate data. |
Trees | Provides classes to define a tree and any constraints on that tree. |
Classes in Trees used by Alignments | |
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Tree
Represents a phylogenetic tree. |
Classes in Trees used by Ancestors | |
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Tree
Represents a phylogenetic tree. |
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TreeException
Exception thrown when there is a problem with a tree |
Classes in Trees used by Constraints | |
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Tree
Represents a phylogenetic tree. |
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TreeException
Exception thrown when there is a problem with a tree |
Classes in Trees used by Likelihood | |
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Branch
Represents a branch in a tree |
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Tree
Represents a phylogenetic tree. |
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TreeException
Exception thrown when there is a problem with a tree |
Classes in Trees used by Optimizers | |
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TreeException
Exception thrown when there is a problem with a tree |
Classes in Trees used by Simulations | |
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Tree
Represents a phylogenetic tree. |
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TreeException
Exception thrown when there is a problem with a tree |
Classes in Trees used by Trees | |
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Branch
Represents a branch in a tree |
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Tree
Represents a phylogenetic tree. |
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TreeException
Exception thrown when there is a problem with a tree |
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