Available Software on the OBCP Cluster

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.

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: 1.7.4
• Parallel: MPI-enabled; BEAGLE threading
• Notes:

BEAUti

• Filename: beauti
• Version: 1.7.4
• Parallel: No
• Notes:

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 Light

• Filename: raxmlLight
• Version: 1.0.8
• Parallel: Pthreads threading
• Notes:

Population Genetic Software

BP&P

• Filename: bpp
• Version: 2.1b
• Parallel: No
• Notes:

Migrate-N

• Filename: migrate-n
• Version: 3.3.1
• Parallel: MPI-enabled
• Notes: