ILRI Research Computing

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

===== Information =====

  * Latest Version: 8.2.12
  * Added: June, 2011
  * Updated: September, 2018
  * Link: https://github.com/stamatak/standard-RAxML

=== Usage ===

Show all available versions of RAxML:

<code>$ module avail RAxML</code>

Load one version into your environment and run it:

<code>$ module load RAxML/8.2.12
$ raxmlHPC-PTHREADS-AVX</code>

Note: you should set the number of concurrent CPU threads using the ''-T'' option. For example, if you have requested five CPUs in your SLURM batch script, you can tell RAxML to use five threads:

<code>$ raxmlHPC-PTHREADS-AVX -T 5</code>

=== Installation ===
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz
$ tar xf v8.2.12.tar.gz
$ cd standard-RAxML-8.2.12
$ make -f Makefile.SSE3.gcc
$ make -f Makefile.SSE3.PTHREADS.gcc
$ make -f Makefile.AVX.gcc
$ make -f Makefile.AVX.PTHREADS.gcc
$ sudo mkdir -p /export/apps/RAxML/8.2.12/bin
$ sudo cp raxmlHPC-* /export/apps/RAxML/8.2.12/bin</code>