Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
Modifier and Type | Class and Description |
---|---|
class |
ConstantPopulation
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
|
class |
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.
|
class |
ConstExpGrowth
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
|
class |
DemographicModel
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
|
class |
ExpandingPopulation
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
|
class |
ExponentialGrowth
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
|
Modifier and Type | Class and Description |
---|---|
class |
ConstantMutationRate
This class models a constant mutation rate
(parameter: mu = mutation rate).
|
class |
MutationRateModel
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
class |
SteppedMutationRate
This class models a step-wise mutation rate.
|
class |
WindowedMutationRate
This class models a windowed mutation rate
(parameter: mu = mutation rate).
|
Modifier and Type | Class and Description |
---|---|
class |
SimpleSummarizable |
Constructor and Description |
---|
SimpleSummarizable(Summarizable toImitate)
The Imitation constructor - for immitating another Summarizable object with
minimum memory requirements
|