Uses of Package
pal.coalescent
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Packages that use pal.coalescent 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. -
Classes in pal.coalescent used by pal.coalescent Class 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) -
Classes in pal.coalescent used by pal.eval Class 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. -
Classes in pal.coalescent used by pal.supgma Class Description 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 Class Description DemographicModel This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.