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RAxML

Randomised Axelerated Maximum Likelihood (RAxML) is a sequential and parallel application for inference of large phylogenies with maximum likelihood.

RAxML is available as a module on Apocrita.

Each RAxML version on Apocrita contains 6 different binaries:

  • raxmlHPC (the standard version)
  • raxmlHPC-SSE3 (runs 40% faster than the non-SSE3 version)
  • raxmlHPC-AVX (runs 10-30% faster than the SSE3 version)
  • MPI versions of the above three applications

To select the appropriate RAxML version, please see the Compiler Instructions page.

Usage

To run the latest installed version of RAxML, simply load the raxml module:

$ module load raxml
$ raxmlHPC-AVX -help

raxmlHPC[-SSE3|-AVX]
      -s sequenceFileName -n outputFileName -m substitutionModel
      [-a weightFileName] [-A secondaryStructureSubstModel]
      [-b bootstrapRandomNumberSeed] [-B wcCriterionThreshold]
      [-c numberOfCategories] [-C] [-d] [-D]
      [-e likelihoodEpsilon] [-E excludeFileName]

For full usage documentation, pass the -help switch to any of the binaries.

Example jobs

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load raxml

raxmlHPC-AVX -m BINGAMMA \
             -p 12345 \
             -s ~/raw_data.phy \
             -n raxml_output_file

MPI job

Here is an example MPI job running on two sdv nodes (48 cores):

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 48
#$ -l infiniband=sdv-i
#$ -l h_rt=1:0:0

module load raxml

raxmlHPC-MPI-AVX -m BINGAMMA \
                 -p 12345 \
                 -s ~/raw_data.phy \
                 -n raxml_output_file
                 -N ${NSLOTS}

References