Bioinformatics Software
The following software packages are installed locally on the BCB computer systems (binf.gmu.edu). Click on package name to access web-based documentation:
| Name | OSX Version | Linux Version |
|---|---|---|
| AutoDock | 3.0.5 | |
| BioConductor | 1.7 | 1.7 |
| BioPerl | 1.5.1 | |
| BLAST | 2.2.13 | |
| ce | 2004-07-06 | |
| CLUSTALW | 1.8.3 | |
| Cn3D | 4.1 | |
| Cross_match | 0.990329 | |
| Dsspcmbi | 2000-01-04 | |
| EMBOSS | 3.0.0 | |
| Glimmer | 2.13 | |
| Gnuplot | 4.0 | 4.0 |
| HMMer | 2.3.2 | |
| Mavid | 2.0.4 | |
| MEME | 2.3.1 | |
| Mfold | 3.1 | |
| Modeller | 8.0 | |
| MUMmer | 3.18 | |
| Multiz | 3.18 | |
| NAMD | 2.5 | 2.5 |
| PHYLIP | 3.65 | |
| Stride | 1 | 1 |
| SWIG | 1.3.25 | 1.3.25 |
| VMD | 1.8.2 | 1.8.3 |
The following compilers are installed locally on the BCB computer systems:
| Name | OSX Version | Linux Version |
|---|---|---|
| c++ | 4.0.0 | 3.3.4 |
| cc | 4.0.0 | 3.3.4 |
| f77 (g77) | 3.4.4 | 3.3.4 |
| gcc | 4.0.0 | 3.3.4 |
| gfortran | 3.5 | 4.2.0 |
| java | 1.4.2-54 | 1.4.2_05 |
| Matlab | 7.0.1.24704 | |
| mpicc | LAM 7.1.1 | |
| mpif77 | LAM 7.1.1 | |
| Perl | 5.8.6 | 5.8.6 |
| Python | 2.3.5 | 2.3.4 |
| R | 2.1.1 | 2.2.1 |
Command Line Help Files
To get a list of all the EMBOSS programs while logged in, do:
% wossname
To access the full online documentation for any of the EMBOSS programs, do:
% tfm program
To check the availability of any Perl module, do:
% perldoc module e.g., % perldoc Bio::Perl
Send requests for installations or upgrades to binf@gmu.edu.