BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.01 beta, April 21, 2004

Generating multiple run control files

To do multiple runs easily with the same run controls, but with different seeds for the random number generator, use the program genrc. The program will generate a set of run control files which share a common base set of run controls but set the seed run control to different values and will use different file-roots for the output files. Since the seeds are different, the runs of badger will generate different MCMC chains. The genrc program takes the name of a base run control file, which contains the run controls common for all runs, the base name for the generated run control files, and, optionally, the base file-root for the output files, the number of run control files to generate, the number of the first run control file to be generated, and a seed for its own random number generator. It creates a set of run control files whose names are the base name followed by the number of the file.

For example, the simplest way to invoke the program is to type:

genrc -i camp.base.rc -r camp.rc

This command will create 5 run control files (camp.rc.0, camp.rc.1, ...) each of which will include the run controls of camp.base.rc but use different seeds. Each run control file will use a different file-root for the output files, namely, run1.0, run1.1, run1.2 and so forth.

The required and optional arguments for genrc are:

Genrc Options

Option	Description
-i (required)	The file containing the common run controls.	-r (required)	The base name of the generated run control files.
-f (optional)	The base name for the output files. run1 is the default.
-n (optional)	The number of run control files to generate. 5 is the default.
-b (optional)	The number of the first run control file generated. 0 is the default.
-s (optional)	The seed for the random number generator used to choose the seeds in the generated run control files. 12345 is the default.

The most general way to call genrc is:

genrc [-h] [--help]
  {-r|--rcfilename} rc-filename
  {-i|--include} include-file
  [-f file-root] [--fileroot file-root]
  [-n number-to-generate] [--number number-to-generate]
  [-b beginning-number] [--begin beginning-number]
  [-s seed] [--seed seed]

The square brackets indicate optional arguments and the braces indicate a choice.

For example, in analyzing the Campanulaceae dataset, we use the following command:

genrc -r camp.rc -f camp.run1 -i camp.base.rc -n 5

to generate 5 run control files.

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