Software resources available at SanfordBurnham. Some of the software is maintained by IT on a server while other titles can be downloaded and used directly from your computer.
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)
- 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).
- 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
- T-Coffee Multiple sequence alignment program for both protein and DNA.
- 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
- Trans-Proteomic Pipeline
- 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
- NMRpipe provides facilities for conversion and processing of 1D-4D NMR spectra
- NMRViewJ A program for the visualization and analysis of NMR datasets