Uses of Package
pal.coalescent

Packages that use pal.coalescent

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.

Classes in pal.coalescent used by pal.coalescent

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)

Classes in pal.coalescent used by pal.eval

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.

Classes in pal.coalescent used by pal.supgma

DemographicModel
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.

Classes in pal.coalescent used by pal.xml

DemographicModel
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.