Uses of Package
pal.mep

Packages that use pal.mep

pal.coalescent	Classes to model population genetic processes using the coalescent.
pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
pal.xml	Utility classes for converting PAL objects to and from XML documents.

Classes in pal.mep used by pal.coalescent

MutationRateModel
This abstract class contains methods that are of general use for modelling mutation rate changes over time.

Classes in pal.mep used by pal.mep

ConstantMutationRate
This class models a constant mutation rate (parameter: mu = mutation rate).

DeltaModel

DeltaModel.Instance

MutationRateModel
This abstract class contains methods that are of general use for modelling mutation rate changes over time.

MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels

WindowedMutationRate
This class models a windowed mutation rate (parameter: mu = mutation rate).

Classes in pal.mep used by pal.supgma

DeltaModel

MutationRateModel
This abstract class contains methods that are of general use for modelling mutation rate changes over time.

MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels

Classes in pal.mep used by pal.tree

MutationRateModel
This abstract class contains methods that are of general use for modelling mutation rate changes over time.

MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels

Classes in pal.mep used by pal.xml

MutationRateModel
This abstract class contains methods that are of general use for modelling mutation rate changes over time.