© Copyright 2000, 2001, Donald Simon & Bret Larget, Department of Mathematics and Computer Science, Duquesne University.
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).
bambe opens five files for output.
By default, these are:
% summarize -n 200 run1.top > run1.sum
discards the first 200 lines of
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
Make sure to be familiar with methods of assessing MCMC convergence before summarizing the run output for inference.
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