badger
are listed
below. Note that two of the files, file-root.prm
and
file-root.tre
, are only created when the run controls print-permutation
and print-all-trees
, respectively, are set to
true
.
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. |