BUCKy 1.2 README
For higher versions, please refer to the user's manual.

INSTALLATION
Pick a directory where you want the BUCKy code to be.
I will call this directory $BUCKY_HOME in this documentation.
To open the compressed tar file with the BUCKy source code and example data,
do these commands.

  cd $BUCKY_HOME
  tar zxf bucky-1.2.tgz

This creates a directory named BUCKy-1.2 with subdirectories BUCKy-1.2/data and BUCKy-1.2/src .

COMPILATION
If you have gcc installed, compile the software with these commands.

  cd $BUCKY_HOME/BUCKy-1.2/src
  make

This will compile programs mbsum and bucky.
I suggest putting copies in ~/bin if this is in your path.

If you do not have gcc installed, you need to find the installer.
On a Macintosh, it may be in Applications/Installers/Developer Tools .

HELP
Type these commands for very brief help messages.

  mbsum --help
  bucky --help

EXAMPLE
Suppose that you have a directory where each file is of the form *.t and is a MrBayes output file.
Use mbsum to summarize each file.  Remove the first 1000 trees of each for burnin.

  for X in *.t; do mbsum -n 1000 $X; done

This will create a file named <filename>.in for each file named <filename>.t .
Warning!  It will overwrite files with the name <filename>.in if they exist.

Next, to run bucky with default parameters, try this.

  bucky *.in

This will create a bunch of output files of the form run1.* .
You can pick your own root file name.

YEAST EXAMPLE
To try the yeast example described in the Ane et-al MBE paper (with a much smaller number of updates),
you can try the following.

  cd $BUCKY_HOME/BUCKy-1.2/data/yeast
  ../../src/bucky y???/*.in

EXAMINING OUTPUT
Mac users who want to use standard Mac applications to read the output can open any of the output files
using TextEdit.

Bret Larget and Cecile Ane
17 January, 2007
Madison, Wisconsin