|
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 |
|
| 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. |