The files created with each run of

`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. |

Back to the table of contents.

This page was most recently updated on June 29, 2004.

badger@badger.duq.edu