See: Description
Interface | Description |
---|---|
CoalescentTree |
interface defining a parameterized tree that
includes demographic information.
|
DemographicTree |
interface defining a parameterized tree that
includes demographic information.
|
Class | Description |
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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.
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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.
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Exception | Description |
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CoalescentException |
Exceptions to do with coalescent models et cetera.
|