RAxML

Description

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.

Home Page

http://www.exelixis-lab.org/

Documentation

https://cme.h-its.org/exelixis//web/software/raxml/index.html#documentation

License

RAxML source code can be downloaded freely from it's website.

Usage

Use

module avail raxml

to see which versions of RAxML are available. Use

module load raxml

or

module load raxml/version

to get access to RAxML.

All version of RAxML are installed:

raxmlHPC               (serial version)
raxmlHPC-SSE3          (serial with SSE3 extensions)
raxmlHPC-AVX           (serial with AVX extensions)
raxmlHPC-PTHREADS      (threaded version)
raxmlHPC-PTHREADS-SSE3 (threaded with SSE3 extensions)
raxmlHPC-PTHREADS-AVX  (threaded with AVX extensions)
raxmlHPC-MPI           (MPI version)
raxmlHPC-MPI-SSE3      (MPI with SSE3 extensions)
raxmlHPC-MPI-AVX       (MPI with AVX extensions)
raxmlHPC-HYBRID        (hybrid version)
raxmlHPC-HYBRID-SSE3   (hybrid with SSE3 extensions)
raxmlHPC-HYBRID-AVX    (hybrid with AVX extensions)

As a rule of thumb performance is best with the executables with AVX enabled.

Running RAxML in a job script is similar to an interactive run:

module load raxml
raxmlHPC-type-extention [parameters]