badger. 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:
badger < defaultrc
The program may be run in background.
badger < defaultrc &
Information on the progress of the run is written to standard output
(normally the screen, unless redirected). The program
badger opens between eight and ten files for output, depending on how the run controls are set.
The root of these files may be changed in the run control file.
To easily do multiple runs with the same run controls, but with
different seeds for the random number generator, use the program
genrc. For example, the command
genrc -i default.base.rc -r default.rc -n 4
will generate 4 run control files (
default.rc.1, ...) all using the run controls of
default.base.rc but using different seeds.
After doing a run, the program
summarize may be used to
tabulate the results. The command
summarize -s 200 run1.top > run1.sum
skips 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,
summarizes the posterior ignoring differences within clades. and
finds a list of the common clades.
A chart to compare the frequencies the common clades from different
summary files can be made, using the
chart run1.sum run2.sum run3.sum run4.sum
Make sure to be familiar with methods of assessing MCMC convergence before summarizing the run output for inference.
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