Package | Description |
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pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Modifier and Type | Class and Description |
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class |
DemographicClockTree
Provides parameter interface to a clock-like genealogy which is
assumed to have some demographic pattern of theta (diversity) as
well as branch parameters (the minimal node height differences
at each internal node).
|
Modifier and Type | Class and Description |
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class |
ClockTree
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node)
|
class |
LogParameterizedTree
This class logarithmically transforms tree parameters.
|
class |
MutationRateModelTree
Provides parameter interface to any clock-like tree with
serially sampled tips (parameters are the minimal node height differences
at each internal node).
|
class |
UnconstrainedTree
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
|
Constructor and Description |
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ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
Cloning constructor
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