| Package | Description |
|---|---|
| pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
| pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
| pal.supgma | |
| pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
| Class and Description |
|---|
| CoalescentIntervals
A series of coalescent intervals representing the time
order information contained in a (serial) clock-constrained
tree.
|
| ConstantPopulation
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
|
| ConstExpGrowth
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
|
| DemographicModel
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
|
| DemographicTree
interface defining a parameterized tree that
includes demographic information.
|
| ExponentialGrowth
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
|
| SerialCoalescentGenerator.Results
A simple wrapper class for containing the results which may either be
a number of trees, or a number of trees and alignments (in parallel arrays)
|
| Class and Description |
|---|
| CoalescentIntervals
A series of coalescent intervals representing the time
order information contained in a (serial) clock-constrained
tree.
|
| DemographicModel
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
|
| Class and Description |
|---|
| DemographicModel
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
|
| Class and Description |
|---|
| DemographicModel
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
|