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. 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.