Class Summary |
AlignColumn |
An AlignColumn is an object that represents an observed or a hidden character
and stores a double array storing the Felsenstein likelihoods. |
AutomateParameters |
A class that contains the logic when to stop the burn-in, sampling, or
how to determine the sampling rate. |
CircularArray<E> |
Dynamically growing circular array with extremely efficient deque and hash operations. |
Input |
This class is an extension of the Postprocess class and is for showing the
actual input sequences. |
InputData |
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MainManager |
This is the central class in the information flow amongst classes. |
Mcmc |
This class handles an MCMC run. |
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. |
TreeAlgo |
|
Utils |
This class contains multi-purpose static functions. |
Vertex |
This is a vertex of the tree. |