PHYLIP is a free package of programs for inferring phylogenies. You can find extensive documentation for PHYLIP here.

1. Upload necessary files onto the HPC

More information on file management, connecting to the hpc and ssh can be found here.

First create a directory called phylip inside your home directory. Upload your infile to that directory. For this example I will use an example file from the PHYLIP documentation.

5   13
Alpha AACGTGGCCAAAT
Beta AAGGTCGCCAAAC
Gamma CATTTCGTCACAA
Delta GGTATTTCGGCCT
Epsilon GGGATCTCGGCCC

After the uploads your should have one file inside your phylip directory.

phylip/infile

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;

3. Submit the job to run on the hpc.

More information on submitting jobs and different MOAB commands can be found here
In order to submit the job to be run on the cluster, use the program msub.

cd ~/phylip
msub dnaml.moab.sh

4. Monitoring the job.

More information on monitoring jobs and different MOAB commands can be found here
In order to see the status of all your jobs at the command line type.

showq -w user=`whoami`

5. Collect the output.

Once the job is funished running there will be outfile and outtree files in the phylip directory. Transfer this file to your desktop computer.