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raxml-software [2015/07/27 10:18]
joguya
raxml-software [2018/09/16 10:45] (current)
aorth
Line 2: Line 2:
 RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. ​ RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. ​
  
-  ​* Latest Version: 8.2.0+===== Information ===== 
 + 
 +  ​* Latest Version: 8.2.12
   * Added: June, 2011   * Added: June, 2011
-  * Updated: ​July2015+  * Updated: ​September2018
   * Link: https://​github.com/​stamatak/​standard-RAxML   * Link: https://​github.com/​stamatak/​standard-RAxML
  
 === Usage === === Usage ===
-  * Show all available versions of RAxML<​code>​module avail RAxML</​code>​ + 
-  ​* ​Load RAxML module: <​code>​module load RAxML/8.2.0</​code>​+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 === === Installation ===
-  *Notes from the sysadmin during installation:<​code>​ +Notes from the sysadmin during installation:​ 
-wget https://​github.com/​stamatak/​standard-RAxML/​archive/​v8.2.0.tar.gz + 
-tar -xvf v8.2.0.tar.gz +<​code>​$ cd /tmp 
-cd standard-RAxML-8.2.0/ +wget https://​github.com/​stamatak/​standard-RAxML/​archive/​v8.2.12.tar.gz 
-make -f Makefile.AVX.gcc +tar xf v8.2.12.tar.gz 
-rm *.o +cd standard-RAxML-8.2.12 
-make -f Makefile.AVX.PTHREADS.gcc +make -f Makefile.SSE3.gcc 
-rm *.+make -f Makefile.SSE3.PTHREADS.gcc 
-module load openmpi/1.8.2 +$ make -f Makefile.AVX.gcc 
-make -f Makefile.MPI.gcc +make -f Makefile.AVX.PTHREADS.gcc 
-rm *.o +sudo mkdir -p /​export/​apps/​RAxML/​8.2.12/bin 
-sudo mkdir -p /​export/​apps/​RAxML/​8.2.0/bin +sudo cp raxmlHPC-* /​export/​apps/​RAxML/​8.2.12/​bin</​code>​
-sudo cp -v raxmlHPC* /​export/​apps/​RAxML/​8.2.0/bin+
-</​code>​+
raxml-software.1437981510.txt.gz · Last modified: 2015/07/27 10:18 by joguya