Package | Description |
---|---|
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 | Description |
---|---|---|
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 | Description |
---|---|---|
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 | Description |
---|---|
ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy) |
Cloning constructor
|