Uses of Package
statalign.base

Packages that use statalign.base

statalign
statalign.base
statalign.base.mcmc
statalign.base.thread
statalign.io.input.plugins
statalign.mcmc
statalign.model.ext
statalign.model.ext.plugins
statalign.model.ext.plugins.structalign
statalign.postprocess
statalign.postprocess.gui
statalign.postprocess.plugins
statalign.postprocess.plugins.structalign
statalign.ui

Classes in statalign.base used by statalign

MainManager
This is the central class in the information flow amongst classes.

Classes in statalign.base used by statalign.base

AlignColumn
An AlignColumn is an object that represents an observed or a hidden character and stores a double array storing the Felsenstein likelihoods.

InputData

MainManager
This is the central class in the information flow amongst classes.

MCMCPars
This is a container class containing the MCMC parameters described below.

McmcStep
Provides information on an MCMC step and additional MCMC statistics.

State
Objects of this class completely describe the state of the MCMC at a certain time.

Tree
This is the current tree in the MCMC run.

Vertex
This is a vertex of the tree.

Classes in statalign.base used by statalign.base.mcmc

Mcmc
This class handles an MCMC run.

Tree
This is the current tree in the MCMC run.

Classes in statalign.base used by statalign.base.thread

MainManager
This is the central class in the information flow amongst classes.

Classes in statalign.base used by statalign.io.input.plugins

Tree
This is the current tree in the MCMC run.

Classes in statalign.base used by statalign.mcmc

Mcmc
This class handles an MCMC run.

Tree
This is the current tree in the MCMC run.

Classes in statalign.base used by statalign.model.ext

InputData

MainManager
This is the central class in the information flow amongst classes.

Mcmc
This class handles an MCMC run.

Tree
This is the current tree in the MCMC run.

Vertex
This is a vertex of the tree.

Classes in statalign.base used by statalign.model.ext.plugins

InputData

Tree
This is the current tree in the MCMC run.

Vertex
This is a vertex of the tree.

Classes in statalign.base used by statalign.model.ext.plugins.structalign

Tree
This is the current tree in the MCMC run.

Vertex
This is a vertex of the tree.

Classes in statalign.base used by statalign.postprocess

InputData

MainManager
This is the central class in the information flow amongst classes.

Mcmc
This class handles an MCMC run.

McmcStep
Provides information on an MCMC step and additional MCMC statistics.

State
Objects of this class completely describe the state of the MCMC at a certain time.

Classes in statalign.base used by statalign.postprocess.gui

MainManager
This is the central class in the information flow amongst classes.

Classes in statalign.base used by statalign.postprocess.plugins

InputData

Mcmc
This class handles an MCMC run.

McmcStep
Provides information on an MCMC step and additional MCMC statistics.

State
Objects of this class completely describe the state of the MCMC at a certain time.

Classes in statalign.base used by statalign.postprocess.plugins.structalign

InputData

McmcStep
Provides information on an MCMC step and additional MCMC statistics.

State
Objects of this class completely describe the state of the MCMC at a certain time.

Classes in statalign.base used by statalign.ui

MainManager
This is the central class in the information flow amongst classes.