BAMBE

Bayesian Analysis in Molecular Biology and Evolution

Version 2.03 beta, January 2001

Running the programs

The main program for sampling trees and parameter values by Markov chain Monte Carlo is bambe. The program expects input to be directed from a run control file, which specifies the name of a data file, an optional tree file, and other run characteristics. If the run control file is named defaultrc, the program is called by:

% bambe < defaultrc

The program may be run in background.

% bambe < defaultrc &

Information on the progress of the run is written to standard output (normally the screen, unless redirected). The program bambe opens five files for output. By default, these are:

run1.lpd
- which stores the log of the unnormalized posterior density at each sample point
run1.par
- which stores parameter values at each sample point
run1.out
- which stores the run characteristics and several data summaries
run1.top
- which stores the tree topology at each sample point
run1.tre
- which stores the final tree.

The root of these files may be changed in the run control file. The command

% summarize -n 200 run1.top > run1.sum

discards the first 200 lines of run1.top, counts and tabulates the number of times each tree topology appears, automatically defines clades and tabulates the transitions between clade subtree topologies, reports the posterior probability of each internal node from the most probable tree topology, and summarizes the posterior ignoring differences within clades. More details on available options are described here.

Make sure to be familiar with methods of assessing MCMC convergence before summarizing the run output for inference.

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This page was most recently updated on January 19, 2001.

bambe@mathcs.duq.edu