RAxML

RAxML

RAxML (Randomized Axelerated Maximum Likelihood) written by Alexandros Stamatakis and others is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

Variations

/apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3	OpenMP threaded version
/apps/RAxML/7.3.0/raxmlHPC-HYBRID-SSE3	OpemMPI/OpenMP MPI and threaded hybrid version

Sample Submission Script for threaded (PTHREADS) version

#!/bin/sh
#PBS -N RAxML
#PBS -m bea
#PBS -M <e-mail>	
#PBS -o pbsJobLog
#PBS -e pbsJobErr
#PBS -l nodes=1:ppn=4
#PBS -l pmem=500mb
#PBS -l walltime=00:05:00
#
# This job's working directory
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`

/apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3 -f a -m GTRGAMMA -s dna.phy -p 12345 -x 12345 -# 100 -n dnaBSML -T 4

# Note the -T 4 option specifying the use of 4 cores, matching the nodes=1:ppn=4 in the #PBS -l statement above