1. Bioshell documentation
    (external links)
    1. Introduction
    2. Installation
    3. Cookbook
    4. Manuals

What is BioShell ?

A set of command-line programs for easy data manipulation from a terminal or a shell script. The programs can read and write standard file formats and handle protein sequences and structures. The tools helps also in simple calculations, like sequence alignment, Phi/Psi angles, crmsd and many more. See Programs page for details.

In the newest version 3.0 of BioShell package, a wide set of test/examples has been also published. Many of these tests are in facts small applications usefull in daily research.

Package history

The first version of the package (BioShell 1.0) was in use in 2004-2006 and was written in C. Later the package was reimplemented in Java as (BioShell 2.0). One of the biggest advantage of that version was that every BioShell classes were accessible as Jython (Python implemented in Java) modules, which resulted in a versetile scripting platform for structural bioinformatics. Recenty the package was rewritten again, back to C++ to improve computational efficiency.