Uses of Package
pal.coalescent

Packages that use pal.coalescent
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
 
Utility classes for converting PAL objects to and from XML documents.
  • Classes in pal.coalescent used by pal.coalescent
    Class
    Description
    A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
    This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
    This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
    This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
    interface defining a parameterized tree that includes demographic information.
    This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
    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
    Class
    Description
    A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
    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
    Class
    Description
    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
    Class
    Description
    This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.