BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Copyright © 2004 by Bret Larget & Don Simon


Output files


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.

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.


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

badger@badger.duq.edu