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