omrokgen

NAME
SYNOPSIS
DESCRIPTION
EXAMPLE
CITE
VERSION
LICENSE
AUTHORS

NAME

omrokgen − randomly change the positions of the nucleotides in a DNA sequence

SYNOPSIS

omrokgen name_of_input_file name_of_output_file number_of_generated_strings

DESCRIPTION

omrokgen reads an input sequence (DNA) and generates a user specified number of new sequences where the positions of the nucleotides are randomly changed. The number of the various nucleotide types in the generated sequences do not vary from the original sequence. The input file should only contain one input sequence. This input sequence can further only contain A, C, G, T in upper case.

The output from omrokgen to standard out is in Norwegian.

EXAMPLE

To generate ten new sequences from the sequence in the input file ’infile’ and write them to the output file ’outfile’, just type:

omrokgen infile outfile 10

CITE

Please cite in the following manner if you choose to use omrokgen:

V. Knudsen and G.Caetano-Anolles, Some title of a paper published in some journal.

VERSION

This man page documents omrokgen version 0.1.

LICENSE

Copyright 1999-2007 by Vegeir Knudsen. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1.

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

DISCLAIMER:

THIS SOFTWARE IS PROVIDED BY THE AUTHOR ‘‘AS IS’’ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

AUTHORS

Vegeir Knudsen and Gustavo Caetano-Anolles.