From Darwin

Contents 1 System software 1.1 Compilers 1.2 Libraries 2 Text editors 3 Bioinformatics Software 3.1 BioRoll 3.2 Other software

System software

Compilers
Name	Location
Intel Fortran 9.1.051	/opt/intel/fc/9.1.051/bin/ifort
Intel C 9.1.051	/opt/intel/cc/9.1.051/bin/icc
GNU C GCC 3.4.6	/usr/bin/gcc
GNU Fortran 77 GCC 3.4.6	/usr/bin/g77
GNU Fortran 90	TBD

Libraries
Name	Location
Intel 9.1.051 build of MPICHMX 1.2.7	/home/ibm/util/mpich-mx-1.2.7..1/icc/9.1.051
GCC build of netCDF 3.6.1	/home/ibm/util/netcdf-3.6.1
GCC build of netCDF 3.6.2	/home/ibm/util/netcdf-3.6.2

Text editors

Bioinformatics Software

BioRoll

The Rocks BioRoll is installed on the cluster providing many commonly used programs for computational biology. The list of installed packages can be found in either of the following:

• BioRoll package list in the online documentation
• The /opt/Bio directory

Some of the major packages are listed below.

• BLAST (both the NCBI and mpi versions are installed) is the primary sequence matching software for bioinformatics.
• bioperl and biopython provide extensive libraries for manipulating bioinformatic data.

Other software

• PhyML
• Muscle
• TreePuzzle
• OrthoMCL
• Paup*