Department of Bioinformatics and Computational Biology

George Mason University

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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.