Description of BADGER output files.
| File |
Description |
file-root.acc |
stores the acceptance probabilities for each chain and each update method
at each sample point. |
file-root.len |
stores the lengths of all branches of the tree at each sample point. |
file-root.lpd |
stores the log of the unnormalized posterior density
at each sample point. |
file-root.lst |
stores the final tree. |
file-root.min |
stores the tree of minimal total branch length found so far along with
the number of the cycle at which it occurred. |
file-root.out |
stores a matrix of reversals distances among the taxa, the run controls used,
the values of mu and psi used, and a table of accepted tree counts for each update method. |
file-root.par |
stores the log-likelihood and the total number of reversals at each sample point. |
file-root.prm |
stores the permutation of an internal node of the tree at each sample point. Most useful when there
are only three taxa in the data set. |
file-root.top |
stores the tree topology at each sample point. |
file-root.tre |
stores the trees at each sample point. |