Utilities on Biowulf

The software listed below is typically single-threaded and not intended for parallel jobs. These programs are installed on Biowulf primarily for the convenience of those who occasionally examine or analyze their results on the main login node. They may also be used in large-scale processing via swarm jobs.

xnview
xnview is a multipurpose image translater/viewer, better than xv. HOWEVER, it will on occasion screw up CMYK color display...

acroread
The standard tool for reading Adobe PDF files.

Grace
Grace is a WYSIWYG 2D plotting tool for the Xwindow system. It is a successor to Xmgr.

Rasmol
Rasmol is a program for molecular graphics visualization

ImageMagick
ImageMagick is a collection of tools and libraries to read, write and manipulate images in over 89 formats.

Ghostscript
Ghostscript is an X11 viewer for Postscript files.

Gnuplot
Gnuplot is a command-driven interactive function plotting program. It can be used to plot 2D and 3D plots in many differen formats.

Physica
Physica is a high level, interactive programming environment with user friendly graphics and sophisticated mathematical analysis capabilities. Over 200 numeric and character functions are provided, as well as over 30 operators, providing all of the operations of simple calculus, along with powerful curve fitting, filtering and smoothing techniques, and employing a dynamic array management scheme allowing arrays limited in size only by system resources. Algebraic expressions of arbitrary complexity are evaluated using a lexical scanner approach. Line graphs, histograms and pie charts, as well as contour, density and surface plots are available. The user interface is a command language with a simple to use and easy to learn syntax, incorporating basic elements of a structured programming language including conditional branching, looping and subroutine calling constructs.

Jim Kent Library jksrc454.zip
A collection of executables from Jim Kent have been compiled on Biowulf. The programs perform a multitude of tasks from simple number crunching to highly specific sequence analysis and database construction. The executables are located in the directory /usr/local/ucsc on Biowulf.

SeqIO - Sequence Format Conversion
Jim Knight's SeqIO package for sequence format conversion. It converts from/to 22 formats, including Genbank, Fasta, GCG and SwissProt.

PROCHECK and PROCHECK-NMR
A suite of programs from Roman Laskowski for assessing the "stereochemical quality" of a given protein structure.