2. Create Submission script.

In addition to creating the MOAB script you must create a script with the keyboard input for whatever Phylip program you are running. The following input will turn on gamma distributed rates, turn on global rearrangements, and change the Transition/Transversion ratio to 3.

t
3
r
g
y
2
3

More information on MOAB scripts can be found here.
More information on editing text files can be found here
Create a text called dnaml.moab.sh in your phylip directory. The contents of this file should look like this.

#!/bin/bash
#
#  Name this job.
#
#MOAB -N dnaml
#
# Run this job in the "backfill" queue. Delete the following line if 
# you expect this to run more than 4 hours.
#
#MOAB -q backfill
#
#  Maximum wallclock time :( Hours : Minutes : Seconds ) 
#  Change this to the maximum length of time you wish your program 
#  to run
#
#MOAB -l walltime=03:00:00
#
#  Join the two output files (standard output and standard error) 
#  into one. Based on the job name, this means the single output file
#  will be called "dnaml.oJOBID" where JOBID is a job id number 
#  assigned when the job is submitted.
#
#MOAB -j oe
#
#  This command moves from your home directory to the directory
#  from which this script was submitted.
#
cd $PBS_O_WORKDIR
#
#  First you have to source the script that sets up the Bio Applications
source /usr/local/profile.d/bio.sh
#  The command to run
dnaml < input

exit;