Difference between revisions of "Available Software on the OBCP Cluster"
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| Line 53: | Line 53: | ||
| − | == Population Genetic Software == | + | == Population Genetic/Genomic Software == |
=== BP&P === | === BP&P === | ||
* ''Filename'': bpp | * ''Filename'': bpp | ||
| Line 77: | Line 77: | ||
* ''Parallel'': MPI-enabled | * ''Parallel'': MPI-enabled | ||
* ''Notes'': This is a beta version | * ''Notes'': This is a beta version | ||
| + | |||
| + | === Stacks === | ||
| + | * ''Filename'': multiple executables | ||
| + | * ''Version'': 0.99998 | ||
| + | * ''Parallel'': OpenMP threading | ||
| + | * ''Notes'': | ||
Revision as of 18:53, 2 May 2013
Available Software on the OBCP Cluster
This section of the wiki is designed to help a user locate particular software that is present on the OBCP cluster. Send any software requests to Joe Cora.
Contents
Introduction
Standard software packages that are present on most Linux operating systems like Python, Perl, R, etc. are already installed on the OBCP cluster. Some software are designed to be run in parallel by using the message passing interface (MPI) and/or through thread support built into the software. For more information on running programs in parallel, visit the Multiple Processor Runs on the OBCP Cluster page.
Phylogenetic Software
BEAST
- Filename: beast
- Version: 2.0.1
- Parallel: MPI-enabled; BEAGLE threading
- Notes:
BEAUti
- Filename: beauti
- Version: 2.0.1
- Parallel: No
- Notes: This program is a BEAST plugin
MrBayes
- Filename: mb
- Version: 3.2.1
- Parallel: MPI-enabled
- Notes: This version of MrBayes as well as 3.1.x do not operate properly on operating systems using the newer Linux kernels. An attempt to address this problem with the authors was fruitless.
RaxML
- Filename: raxml
- Version: 7.3.1
- Parallel: Pthreads threading
- Notes:
RaxML Light
- Filename: raxmlLight
- Version: 1.0.8
- Parallel: Pthreads threading
- Notes:
SNAPP
- Filename: snapp
- Version: 1.1.1
- Parallel: MPI-enabled; BEAGLE threading
- Notes: This program is a BEAST plugin
Genomic Software
Oases
- Filename: oases
- Version: 0.2
- Parallel: OpenMP threading
- Notes: Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.
Velvet
- Filename: velveth & velvetg
- Version: 1.2.08
- Parallel: OpenMP threading
- Notes: Default parameters were used with the exception of enabling OpenMP. Velvet should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.
Population Genetic/Genomic Software
BP&P
- Filename: bpp
- Version: 2.1b
- Parallel: No
- Notes:
IMa2
- Filename: IMa2
- Version: 8.27.12
- Parallel: No
- Notes: version is the date of release (August 27, 2012)
Migrate-N
- Filename: migrate-n
- Version: 3.3.1
- Parallel: MPI-enabled
- Notes:
Migrate-N (beta)
- Filename: migrate-n-beta
- Version: 3.4.4
- Parallel: MPI-enabled
- Notes: This is a beta version
Stacks
- Filename: multiple executables
- Version: 0.99998
- Parallel: OpenMP threading
- Notes:
