RAxML

From ScientificComputing
Jump to: navigation, search

Category

Bioinformatics

Description

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

Available versions

Legacy versions Supported versions New versions
8.2.4

Environment modules

Version Module load command Additional modules loaded automatically
8.2.4 module load gcc/4.8.2 open_mpi/1.6.5 raxml/8.2.4

How to submit a job

You can submit a RAxML job in batch mode with the following command:
bsub [LSF options] "raxmlHPC-HYBRID-AVX [raxml options]"

or

bsub [LSF options] "raxmlHPC-PTHREADS-AVX [raxml options]
Here you need to replace [raxml options] with raxml command line options (please run raxmlHPC-HYBRID-AVX -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.

License information

GPLv3

Links

http://sco.h-its.org/exelixis/web/software/raxml

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf
https://github.com/stamatak/standard-RAxML