RAxML-Teaching

Category

Bioinformatics

Program On

Teaching

Version

8.2.11

Author / Distributor

RAxML

Description

"RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." More details are at RAxML

Running Program

The last version of this application is at /usr/local/apps/eb/RAxML/8.2.11-foss-2016b-mpi-sse3

To use this version, please load the module with

ml RAxML/8.2.11-foss-2016b-mpi-sse3 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_RAxML
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=RAxML.%j.out

cd $SLURM_SUBMIT_DIR
ml RAxML/8.2.11-foss-2016b-mpi-sse3
raxmlHPC-PTHREADS-AVX [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml RAxML/8.2.11-foss-2016b-mpi-sse3 
raxmlHPC-PTHREADS-AVX raxmlHPC-PTHREADS-AVX -help

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Installation

Source code is obtained from RAxML

System

64-bit Linux