HPC has installed a variety of phylogenetic software package.  I usually run the parallel version of raxml (mpiraxml), mrbayes (mb_p), and Garli (pargarli) using the MOAB scheduler. Whenever I'm running a version of these packages that is single threaded, I typically run these using Condor.  PAUP and Phylip are only available as single threaded applications, so I typically run these by using Condor. You can find examples of both job submission mechanisms (MOAB and Condor) on the HPC web site under software.  Also, there are some video tutorials on the HPC web (under tutorials) for each job submission mechanism.