Bayesian Analysis in Molecular Biology and Evolution
Version 2.03 beta, January 2001
© Copyright 2000, 2001, Donald Simon & Bret Larget,
Department of Mathematics and Computer Science, Duquesne University.
The files created with each run of
Description of BAMBE output files.
|stores the log of the unnormalized posterior density
at each sample point
|stores parameter values at each sample point
|stores the tree topology at each sample point
|stores the run characteristics and several data summaries
|which stores the final tree
- file-root.par has on each line in this order:
- cycle number
- log likelihood
- tree acceptance proportion in most recent
- parameter acceptance proportion in most recent
- tree height (molecular clock) or half tree diameter (non-clock model)
- global tuning parameter
- eight parameters for each site-category
- file-root.out contains sections:
- Data summary with:
- number of taxa
- total number of sites
- total number of unique sites.
Two identical sites in different categories are considered to be different.
The symbols `-', `N', `X', and `?' are all identical for this purpose.
- Constant site information by category.
- Overall appearance of each symbol.
(The symbols `-', `N', `X', and `?' are all identical for this purpose.)
- Appearance of each symbol by category
and initial pi values from observed frequencies.
- Frequency of bases by taxon.
- Taxon names.
- Run settings.
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This page was most recently updated on January 19, 2001.