| Package | Description |
|---|---|
| pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
| pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
| pal.supgma | |
| pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
| pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
| Class and Description |
|---|
| MutationRateModel
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
| Class and Description |
|---|
| ConstantMutationRate
This class models a constant mutation rate
(parameter: mu = mutation rate).
|
| DeltaModel |
| DeltaModel.Instance |
| MutationRateModel
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
| MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels
|
| WindowedMutationRate
This class models a windowed mutation rate
(parameter: mu = mutation rate).
|
| Class and Description |
|---|
| DeltaModel |
| MutationRateModel
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
| MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels
|
| Class and Description |
|---|
| MutationRateModel
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
| MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels
|
| Class and Description |
|---|
| MutationRateModel
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|