BioShell documentation page

This page provides documentation for the yet unrealeased BioShell package version 3.0 beta. Documentation for version 2.2 (in JAVA) can be found on this page.

Installation guide

Provides instructions how to download, compile and install the package

BioShell programs

So far the following programs are available in the new verion of BioShell:

  • acorr - calculates autocorrelations based on given scalar and vector - type observables
  • hist - prepares 1D histograms
  • seqc - converts between sequence formats, such as FASTA, PIR, SEQ
  • strc - structure converter utility, e.g. extracts chains from PDB
  • str_calc - calculates various structural parameters, such as angles, distaces, etc.
  • str_align - basic calculations on biomolecular structures. Evaluates angles, distances, contacts etc.
  • alignc - calculates alignment between sequences or sequence profiles; also converts between sequence alignment file formats
  • blast_analyse - analyses multiple output files from (Psi)Blast

To see options available for a given program, click on a ling above, or run it in a terminal with -h option, e.g. str_calc -h. Also , you may want to browse the cookbook to see what you can brew with these tools.

BioShell Cookbook

Handy one-liners to solve daily problems. Shows how to convert file formats, perform basic calculations, run clustering etc.

BioShell API documentation

API documentation for the C++ BioShell library