Below is a list of software organized by category: 

Systems biology software and toold

• We use: Ingenuity IPA, MetaCore (Thomson Reuters), NextBio, GeneSpring, TRANSFAC and Oncomine. 
  

Statistical analysis software

• We use: R, Partek, SAS and Excel data analysis toolpak
• Available for use by other researchers at SBMRI: GraphPad Prizm (contact IT for install help) and Excel data analysis toolpak (see here how to load it)

DNA

• Artemis - a desktop DNA sequence viewer and annotation tool (PC and Mac).
  
• Staden Package Package for DNA sequence preprocessing, assembly and editing.
• RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
• Oligo is a desktop program for primer design and analysis (PC and Mac).
  

Protein

• Dotter  Creates dot-plot similarity matrix between DNA-DNA, protein-protein and DNA-protein sequences
• Blast  A suite of programs for searching DNA/protein sequence databases

Alignment

• T-Coffee Multiple sequence alignment program for both protein and DNA.

Phylogeny

• MrBayes Estimate phyolgenetic relationships using Bayesian statistics.
• ATV Java tool for the visualization of annotated phylogenetic trees.

3D Molecular Structure

• PyMol Visually sophisticated tool for creating publication or presentation quality 3D images of molecular structures.
• RasMol Simple but powerful desktop structure visualization and annotation tool.  Runs on PC, Mac, Unix.
  

Microarray and Gene Expression

• GeneSpring
• BioConductor
• GenePattern
  

Proteomics

• GenePattern
• Mascot
• Trans-Proteomic Pipeline
  

Crystallography

• ccp4
• CNSsolve
• HKL
• O
• Resolve Electron density map improvement
• SHARP/autoSHARP Phasing program for multiple wavelenth data sets
• Shelx97 Structure determination suite
• Solve Automated structure determination from MIR, SAD or MAD data
• XDS x-ray detector sofware for monochromatic data

NMR

• NMRpipe provides facilities for conversion and processing of 1D-4D NMR spectra
• NMRViewJ A program for the visualization and analysis of NMR datasets