SYNOPSIS [options] <input_file>

    --help -h       brief help message
    --man           full documentation
    --debug         output running info
    -n <run-num>           the number of converging initial runs
    -l <running-level>           running level
       0          new run
       1          old run with new number of generations
       2          just retrieve data from existing files
    -b <burin-in> the number of burnin generations
    -m <monitor>  the number of monitoring generations
    -v            print version information and quit


 create ancestral intron states based on an alignment and tree
 in a nexus file. The BUGS program will run many times with small
 number of generations to find those can converge (to global optimum)
 and then run one with a large number of generations (convergence)
 the ancestral states will be computed from the average value of 
 those generations and write back to file in history block


BUGS must be installed for running this program.


$Revision: 1.8 $


Chengzhi Liang <>