Package pal.coalescent

Classes to model population genetic processes using the coalescent.

See:
Description

Interface Summary

CoalescentTree	interface defining a parameterized tree that includes demographic information.
DemographicTree	interface defining a parameterized tree that includes demographic information.

Class Summary

CoalescentIntervals	A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
CoalescentSimulator	Simulates a set of coalescent intervals given a demographic model.
ConstantPopulation	This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
ConstExpConst	This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.
ConstExpGrowth	This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
DemographicClockTree	Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
DemographicModel	This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
ExpandingPopulation	This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
ExponentialGrowth	This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
IntervalsExtractor	A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
SerialCoalescentGenerator
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)
SerialCoalescentSimulator	Simulates a set of coalescent intervals given a demographic model.
SkylinePlot	Skyline plot derived from a strictly bifurcating tree or a coalescent interval.

Exception Summary

CoalescentException

Exceptions to do with coalescent models et cetera.

Package pal.coalescent Description

Classes to model population genetic processes using the coalescent.