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--- raxml-software [2014/12/08 10:06] – joguya
+++ raxml-software [2018/09/16 07:45] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== RAxML ======
+RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
-===== RAxML 8.0.23 =====
+===== Information =====
-==== Information ====
-  * Version: 8.0.23
+  * Latest Version: 8.2.12
   * Added: June, 2011
-  * Updated: May 27, 2014
+  * Updated: September, 2018
   * Link: https://github.com/stamatak/standard-RAxML
-===== Usage =====
+=== Usage ===
-=== See versions of RAxML which are available ===
+Show all available versions of RAxML:
-<code>module avail RAxML</code>
-===== Installation ======
+<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>git clone https://github.com/stamatak/standard-RAxML.git
+<code>$ cd /tmp
-cd standard-RAxML
+$ wget https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz
-scl enable devtoolset-1.1 bash
+$ tar xf v8.2.12.tar.gz
-git checkout v8.0.23
+$ cd standard-RAxML-8.2.12
-make -f Makefile.AVX.gcc
+$ make -f Makefile.SSE3.gcc
-rm *.o
+$ make -f Makefile.SSE3.PTHREADS.gcc
-make -f Makefile.AVX.PTHREADS.gcc
+$ make -f Makefile.AVX.gcc
-sudo mkdir -p /export/apps/RAxML/8.0.23/bin
+$ make -f Makefile.AVX.PTHREADS.gcc
-sudo cp raxmlHPC-* /export/apps/RAxML/8.0.23/bin/</code>
+$ sudo mkdir -p /export/apps/RAxML/8.2.12/bin
+$ sudo cp raxmlHPC-* /export/apps/RAxML/8.2.12/bin</code>