Alphabetical list of Software

AMBER    BLAST    ClustalW    DeCypher    EMBOSS    GAUSSIAN03
GENESIS    MapMan    MatLab    NAMD    PGENESIS    R    RepeatMasker    SAS    WU-BLAST


AMBER (Assisted Model Building with Energy Refinement) is a package of molecular simulation programs.  How to run AMBER

BLAST (Basic Local Alignment Search Tool) aligns biological sequences locally and rapidly using heuristic techniques to speed the search.  Access is by command line on lewis, clark, and beagle.  Scripts are available to facilitate BLAST on beagle and clark.  For Lewis see How to run BLAST on Lewis.  For a list of databases to query go here.

ClustalW for multiple sequence alignment.  (Also available in the DeCypher package.)   How to run ClustalW

DeCypher is a suite of programs for biological sequence alignment that uses a combination of optimized algorithms and customized hardware to allow very rapid searches of public and custom databases.  It includes, among other things, all flavors of BLAST, HMM-based profile searches, the Smith-Waterman procedure, and frameshift tolerant alignments to find more distantly related sequences.  Access to DeCypher is through a web page to Discovery.  About DeCypher

EMBOSS The "European Molecular Biology Open Software Suite" contains many tools for sequence alignment and other biological tasks.  To use an EMBOSS program, or the related EMBASSY programs, you need to have emboss in your path or use the path to the command, e.g., "/usr/local/emboss/bin/palindrome" will return a prompt for you to input information to find palindromes in a sequence.  To see the list of EMBOSS and EMBASSY tools on beagle use "ls /usr/local/emboss/bin/".  For documentation about the individual EMBOSS programs go here.  Documentation for the EMBASSY tools may be found here.

GAUSSIAN03 Gaussian predicts the energies, structures, and vibrational frequencies of molecules.  The structures and reactions of even unstable molecules can be studied under a wide range of conditions. How to run GAUSSIAN03 on Clark

GENESIS   (short for GEneral NEural SImulation System) is used for the construction of biologically realistic neural models.  Tutorials for GENESIS may be found here.   Help with running GENESIS on Lewis may be found here.    (If you are using MS Windows you will need to install Xwindows to see the graphical display.)

MapMan   is a tool for projecting the results of gene expression studies onto known metabolic and signaling pathway maps.  This manner of visualization can help summarize results quickly and reveal new relationships among gene products.  How to use MapMan   (If you are using MS Windows you will need to install Xwindows to see the graphical display.)

MATLAB stands for matrix laboratory and is an interactive programming language and numerical computing environment.  Documentation for MATLAB may be found here.   Go here to learn how to use MATLAB on Lewis. (If you are using MS Windows you will need to install Xwindows to see the graphical display.)

NAMD (NAnoscale Molecular Dynamics) allows high-performance simulation of large biomolecular systems written using the Charm++ parallel programming model. How to run NAMD on Lewis

PGENESIS   (short for Parallel GEneral NEural SImulation System) is a parallelized version of GENESIS. (See above.)  Help with running GENESIS or PGENESIS on Lewis may be found here.

R   "R is a language and environment for statistical computing and graphics. ...R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible."   How to use R on Lewis   (If you are using MS Windows you will need to install Xwindows to see the graphical display.)

RepeatMasker Checks DNA sequences for repeat and low complexity DNA sequences and outputs a detailed annotation of the repeats found as well as a modified version of the sequence in which all the annotated repeats have been masked. RepeatMasker uses repeat information derived from RepBase which is maintained locally. Directions for use can be obtained by typing "RepeatMasker" at the command prompt.

SAS   How to use SAS on Clark or Lewis.

WU-BLAST (Washington University BLAST) aligns biological sequences locally and rapidly using heuristic techniques to speed the search.  WU-BLAST allows more tweaking of parameters than does (NCBI) BLAST.   Access is by command line on beagle and lewis.  How to run WU-BLAST