Table of Installed Applications

The packages listed below are installed by the CLAS Linux Group. The staff will support them to the best of their ability. However, the CLAS Linux Group does not have expertise using most of the software listed and may only be able to verify that the software runs.

Linux comes with many packages, and several packages that Linux does not provide are also installed. To find out what packages have been installed on a particular workstation, see What software can I use? in the Frequently Asked Questions.

Chat Clients

Computer Science Software

Document Viewers

Email Clients

  • Alpine - text-interface email and news reader
  • Evolution - Microsoft Exchange-compatible mail and calendaring client
  • Thunderbird - GUI email client

File Archiving and Compression

File Managers


  • The GIMP - the GNU Image Manipulation Program, a powerful, free image editor
  • gnuplot - command line graphing utility
  • Graphviz - a collection of tools for the manipulation and layout of graphs (as in nodes and edges, not as in barcharts).
  • Ipe - create figures in PDF or Encapsulated PostScript
  • Netpbm - toolkit for manipulating images


Mathematical Software

  • COPASI - mathematical modeling of biologic systems
  • Evolver - modeling of surfaces shaped by surface tension and other energies
  • GAP - Groups, Algorithms, Programming system for computational discrete algebra
  • Geomview - interactively view and manipulate 3D objects
  • GNU Octave - graphical numerical computation application
  • Knotplot - knot visualization and manipulation
  • Maple - computer algebra system
  • Mathematica - computational software
  • MathML fonts - fonts for rendering mathematical symbols in Mozilla Firefox-based browsers and LyX
  • Matlab - multi-paradigm numerical computing environment and fourth-generation programming language (Type ver in the Matlab Command Window to see what toolboxes are available.)
    • SeDuMi - (Matlab add-on) software for optimization over symmetric cones
  • XPP-Aut - software for solving differential equations


Remote Access



Statistical Software

  • OpenBugs - perform Bayesian inference Using Gibbs Sampling
  • R - a free software environment for statistical computing and graphics:
    • RStudio - an integrated development interface for R
  • SAS - advanced analytics, business intelligence, data management, and predictive analytics
  • xlispstat - extensible environment for data analysis, statistical instruction and research

System Software

Text Editors

  • Emacs, including modes and plugins:
    • AUCTeX - an emacs TeX/LaTex mode
    • ESS - Emacs Speaks Statistics, support for various statistical packages from within emacs
  • gedit - GNOME editor
  • Kate - KDE editor
  • nano - GNU pico-like editor
  • vim - vi-like editor


Word Processing

  • LaTeX and Tex software
    • dvips - convert DVI to PostScript
    • IPE - a drawing editor for creating figures in PDF or (E)PS format
    • Kile - integrated LaTeX environment/editor, similar to WinEdt
    • LyX - GUI front end for TeX
    • LaTeX Beamer Class - LaTeX class for creating slides and presentations
    • Texmaker - cross-platform LaTeX editor
    • xtex - an interface to DVI and PostScript utilities
  • LibreOffice Writer - free Microsoft Word-compatible word processor