Package pal.coalescent
Classes to model population genetic processes using the coalescent.
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Interface Summary Interface Description CoalescentTree interface defining a parameterized tree that includes demographic information.DemographicTree interface defining a parameterized tree that includes demographic information. -
Class Summary Class Description 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 Exception Description CoalescentException Exceptions to do with coalescent models et cetera.