RAxML
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Description
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.
Required Modules
Serial
- raxml
Parallel (MPI)
- intel
- openmpi
- raxml
System Variables
- HPC_{{#uppercase:raxml}}_DIR - installation directory
PBS Script Examples
{{#fileAnchor: raxml.threaded.pbs}} Download raw source of the [{{#fileLink: raxml.threaded.pbs}} raxml.threaded.pbs]
#!/bin/sh
#PBS -N RAxML
#PBS -m bea
#PBS -M <YOUR E-MAIL HERE>
#PBS -o raxml.$PBS_JOBID.out
#PBS -e raxml.$PBS_JOBID.err
#PBS -l nodes=1:ppn=4
#PBS -l pmem=450mb
#PBS -l walltime=24:00:00
#
# Change to the directory where you type qsub. Should be in /scratch, not your $HOME
cd $PBS_O_WORKDIR
# Load the raxml environment
module load raxml
# The raxml command, modify as needed. Read the manual or use raxmlHPC-PTHREADS-SSE3 -help to see options
# Note the use of the variable $PBS_NP defined by the scheduler based on your resource request
raxmlHPC-PTHREADS-SSE3 -f d -m GTRCAT -s your_data.phy -n output_name -p 3112 -b 758 -N 500 -T $PBS_NP