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MSI Software
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Netfinity Linux Cluster

Complete Software Listing at MSI

ARPACK
454/Roche Genome Sequencer FLX Assembler, Mapper, and Amplicon Variant Analyzer
ABAQUS
ABINIT
Accelrys GCG Wisconsin Package
ACDLabs
ACES II
ACT: a DNA Sequence Comparision Viewer
Adams
Adifor
Adobe Photoshop
AFABC - Program to Analyze Genotypic Data
AMBER
Amira
AMSOL
Analyst QS for Proteomics
Analyst with Bioanalyst for Proteomics
Analyze
ANSIG
ANSOFT: HFSS and Maxwell 3D
ANSYS
ANSYS CFX/ICEM/Workbench
APBS
Apollo
Arachne
ARIA
Artemis
AutoDock
AutoDock Tools
Avizo
Babel
BEAMnrc
Biobase TRANSFAC Database Access
Bioconductor
BioJava
Bioperl
Blas
Blat - Sequence Alignment Tool
Blender
BlueFuse
Bob/AnimaBob
CAChe
Cambridge Structural Database
CAP3 - Contig Assembly Program
CCP4
CCP4mg
Cerius2
CFD-ACE
CHARMM
Chemkin
Chemoffice Ultra
Chimera
Clinprotools - Biomarker discovery with Mass Spec Data
Clover
ClustalW/X - Multiple Sequence Alignment Program
CNS
Comsol Multiphysics/Femlab
Coot
CP2K
CRYSTAL
CVD
DAKOTA
DB2
dChip
ddd
DEJAVU and RAVE
DelPhi
Discovery Studio
DNAStar - Lasergene for Sequence Analysis
Dock
DS Gene - Software for Nucleic Acid and Protein Sequence Analysis
DVD StudioPro
DYTRAN
EASY5
Eclipse
EISPACK
elm
emacs
EMBOSS (The European Molecular Biology Open Software Suite)
Ensight
ESSL
Expressionist - Microarray Data Analysis System
FAST
FASTA - Sequence Analysis Program
FASTLINK - Improved version of LINKAGE
FFTW
FHI98md
FIDAP
Final Cut Pro
FLUENT
FPC - FingerPrinted Contigs
FTDOCK
GAMBIT
GAMESS
GAMESSPLUS
GAMOLA
Gaussian 03
Gaussian98
GaussView
gcc
GCOS - Affymetrix GeneChip Operating Software
GDB
GENECONV - Gene Conversion Detection Program
GeneHunter - Linkage Analysis Program
GeneMapper - Genotyping Software
GenePix
GeneSpring - Microarray Data Analysis Software
GeneTraffic - Microarray Data Analysis Program
GenScan
GenVision for Genomic Data
Geomview
Ghostscript/Ghostview/GV
Gimp
Glimmer
GlimmerM
Global Array Toolkit
Gnuplot
gOpenMol
GOTO BLAS Library
Grace
GRAMM
GRASP
GRASS
Gridgen
GridPro
GROMACS
gsl
HADDOCK
Haploview -- Haplotype analysis
Harpoon
HBPLUS
HDF
HEAsoft
HelixTree - Genetics Analysis Software
Hmmer
Huygens
HYPERWORKS
IBM Data Visualization Explorer
IDL
Igor
ILOG: CPLEX and AMPL
Image - Program for Restriction Digest Gel Images
ImageJ
ImageMagick
Imaris
Imgworks, Imgview, Imgcopy, Imginfo, and Imgformats
Inforsense KDE
Ingenuity Pathways Analysis (IPA)
InsightII
InterProscan - Protein Motif Search Tools
Ipaste, Iblend, blend, Iflip, Iroll
Ivview, Ivcat,Ivfix, ...
Jade
Jaguar
Jmol
JMP
JoinMap
Lahey
LAPACK
LAPACK95
LaTex
LIGPLOT
LINPACK
LS-DYNA
Lucy - Sequence Quality Trimming and Vector Removal
MacroModel
MacVector - Sequence Analysis Software for Macintosh
Maestro
Mapmaker/QTL
Marc/Mentat
Mascot - Search Engine for Mass Spectrometry Data
MASS
MassARRAY Typer Genotyping Software
Materials Studio
Mathematica
Matlab
Matlab Bioinformatics Toolbox
MatlabMPI
Maya
Mediaconvert
MEGA - Molecular Evolutionary Genetics Analysis
MemeMast
Merlin - Linkage Analysis Program
meta-MEME - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins
MetaCore - Metabolic Database Search Tool
Metamorph
Mfold
Microsoft SQL Server
MIDAS Plus
Migrate - Softawre for estimation of migration rate and effective population size
Mimics
Miriad
MKL
MMTSB
MN-GFM
MN-GSM
Modeler
MODELLER
MOE
Molcas
Molden
Molekel
MolMol
MOLPRO
MolScript
MOPAC
Movieconvert
Moviemaker
Movieplayer
MPI
Mplus
MrBayes
Multidivtime
MUMmer - Proram for Aligning Genome Sequences
Muscle - Program for Mutliple Sequence Alignment
mutt
MySQL - Database Management System
Naccess
NAG Libraries
NAMD
Nastran
NBO
NBOView
NCBI BLAST - Basic Local Alignment Search Tool
NEdit
netcdf
NEURON
NMR Pipe
NMRView
NONMEM
NWChem
O
ooffice
Oracle - Database Management System
PALES
PAML - Program for Phylogenetic Analyses of DNA or Protein
PathwayStudio
PATRAN
PAUP
pdb2pqr
PEAKS for Proteomics
PESSL
PFAAT
PGI CDK
pgplot
Phred Phrap Consed
PHYLIP - Program for Evolution Analysis
Picky - Oligo Design Program
pine
PIPP
Plato - Program for Evolution Analysis
Plink --- genotype/phenotype analysis
PolyPhred - Program for SNP
PQS
Primer Express
Primer3 - Primer Design Program
Pro ID For Proteomics
Pro QUANT for Proteomics
PROCHECK
ProFit
PROMOTIF
Pronto 3D2
protarch
ProteinPilot for QSTAR/QTRAP
ProteinShop
ProTS Data - Program for Mass Spectrometry
PWscf
PyMOL
Qt
QUANTA
R
r8s
RasMol
Raster3D
Readseq
Reticulate - Program for Calculating and Displaying Compatibility Matrices
Ribbons
Ricardo
RPluto
S+ArrayAnalyzer - Microarray Data Analysis Module
S-PLUS
SAM - Sequence Alignment and Modeling system
SAM - Significance Analysis of Microarrays
SAS
Scaffold for Proteomics
ScaLAPACK
Schrodinger
SCSL
SCWRL
Sequencher - DNA software for sequencing
SETOR
SHELX
Siesta
SOFY
SOLVE
Sparky
SpeedShop
Spock
Spotfire
SPRNG
SPSS
Staden Package - Sequence Data Handling and Analysis Tools
Star-P
staroffice
Stata
Swiss-PDB
Sybyl
T-coffee - Multiple Sequence Alignment Program
Tecplot
Tgif
To/From Image Tools
Totalview
Tree-Puzzle - Maximum Likelihood Analysis for Nucleotide and Amino Acid
TreeView - Program for Displaying Phylogenies
TribeMCL - Program for clustering proteins into related groups
Trilinos
tRNAscan
TURBOMOLE
Uppsala Software Factory
ViewMol
vim
VMD
VMD-Xplor
VNMR
Volocity
Weka
What Check
WHAT IF
WRF
WSMP: Watson Sparse Matrix Package
WU BLAST- Basic Local Alignment Search Tool
X! Tandem
X-PLOR
xdbx
Xj3D
xlc
xprofiler
XtalView
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