Open Office is an open-source alternative to the Microsoft Office suite of programs. It is compatible with the Microsoft file formats and can run on any modern operating system.
The R Project for Statistical Computing is a free, open-source software package/programming language with a powerful statistical library. It is currently used in several statistics classes at WVU and has extensive documentation/tutorials available. It is known for its powerful graphics capabilities and also has many bioinformatics packages available.
GIMP is a free, open-source graphics design program with capabilities comparable to Photoshop. It has a variety of free, user-created plug-ins available for specific jobs, and users may write their own plug-ins using Script-Fu (Scheme), Perl, or Python. The website contains very straightforward documentation and many “cookbook-style” tutorials.
Octave is a free, open-source software package with a built in programming language for numerical computation. It is often used as a free alternative to the proprietary MATLAB.
LaTeX is a free typesetting system with many different implementations available. It is optimized for technical writing and can be linked with other open source programs (Python, R, etc.) for automatic documentation. Also, no more tangling with Microsoft Equation Editor!
Python is a powerful, object-oriented programming language with a wonderful bioinformatics library (see below). It comes with a GUI interpreter to test out functions in real time without having to use the command line.
BioPython is a bioinformatics library for the Python programming language. It allows many routine bioinformatics routines such as sequence retrieval from GenBank, file conversion, and sequence manipulations to be automated with ease. It also includes many more advanced classes for more complex analyses (i.e. neural networks and genetic algorithms).
