raxml-software
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raxml-software [2014/12/08 10:12] – [Installation Notes] joguya | raxml-software [2018/09/16 07:02] – aorth | ||
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====== RAxML ====== | ====== 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 |
* Added: June, 2011 | * Added: June, 2011 | ||
- | * Updated: | + | * Updated: |
* Link: https:// | * Link: https:// | ||
- | ==== Usage ==== | + | === Usage === |
+ | * Show all available versions of RAxML< | ||
+ | * Load RAxML module: < | ||
- | === See versions of RAxML which are available === | + | === Installation === |
- | < | + | *Notes from the sysadmin during installation:< |
- | + | wget https:// | |
- | ==== Installation | + | tar -xvf v8.2.0.tar.gz |
- | Notes from the sysadmin during installation: | + | cd standard-RAxML-8.2.0/ |
- | + | ||
- | < | + | |
- | cd standard-RAxML | + | |
- | scl enable devtoolset-1.1 bash | + | |
- | git checkout v8.0.23 | + | |
make -f Makefile.AVX.gcc | make -f Makefile.AVX.gcc | ||
rm *.o | rm *.o | ||
make -f Makefile.AVX.PTHREADS.gcc | make -f Makefile.AVX.PTHREADS.gcc | ||
- | sudo mkdir -p / | ||
- | sudo cp raxmlHPC-* / | ||
- | ===== RAxML 8.1.9 ===== | ||
- | Information: | ||
- | * Version: 8.1.9 | ||
- | * Added: December, 2014 | ||
- | * Link: https:// | ||
- | |||
- | ==== Installation Notes ==== | ||
- | * Download pandaseq 2.8.1, create version specific dir in / | ||
- | git clone https:// | ||
- | cd standard-RAxML | ||
- | scl enable devtoolset-1.1 bash | ||
- | git checkout v8.1.9 | ||
- | make -f Makefile.gcc | ||
- | rm *.o | ||
- | make -f Makefile.SSE3.gcc | ||
- | rm *.o | ||
- | make -f Makefile.AVX.gcc | ||
- | rm *.o | ||
- | make -f Makefile.PTHREADS.gcc | ||
- | rm *.o | ||
- | make -f Makefile.AVX.PTHREADS.gcc | ||
- | rm *.o | ||
- | make -f Makefile.SSE3.PTHREADS.gcc | ||
rm *.o | rm *.o | ||
module load openmpi/ | module load openmpi/ | ||
make -f Makefile.MPI.gcc | make -f Makefile.MPI.gcc | ||
rm *.o | rm *.o | ||
- | make -f Makefile.SSE3.MPI.gcc | + | sudo mkdir -p / |
- | rm *.o | + | sudo cp -v raxmlHPC* / |
- | make -f Makefile.AVX.MPI.gcc | + | |
- | rm *.o | + | |
- | sudo mkdir -p / | + | |
- | sudo cp raxmlHPC* / | + | |
</ | </ | ||
- | |||
- | * RAxML/8.1.9 module file:< | ||
- | ##################################################################### | ||
- | ## | ||
- | ## RAxML Modulefile | ||
- | ## by James Oguya, < | ||
- | ## December, 2014 | ||
- | ## | ||
- | |||
- | set | ||
- | set | ||
- | set | ||
- | set | ||
- | |||
- | conflict | ||
- | |||
- | prepend-path | ||
- | </ | ||
- | |||
- |
raxml-software.txt · Last modified: 2018/09/16 07:45 by aorth