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VARNA is a tool for the automated drawing, visualization and annotation of the
secondary structure of RNA, designed as a companion software for web servers
and databases.
Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
electronic mail : Yann.Ponty@lri.fr
paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France
The latest version of this software can be found at:
http://varna.lri.fr
%%%%%%%%%%%%%%%%%%%%%%%%% INVOKING THE GUI VERSION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
A basic editor demonstrating the features of VARNA can be spawned through the
following command:
java -jar VARNAv3-1.jar applis.VARNAGUI
%%%%%%%%%%%%%%%%%%%%%% INVOKING COMMAND LINE VERSION %%%%%%%%%%%%%%%%%%%%%%%%%%%%
VARNA can also be used as a standalone application for producing pictures. For
such an application, the VARNAcmd class was coded, and should be invoked in
the following way:
java -jar VARNAv3-1.jar applis.VARNAcmd
[-i inputFile|-sequenceDBN XXX -structureDBN YYY] -o outFile [opts]
Where:
* inFile: An input file using one of the supported formats (Vienna, CT, BPSeq or RNAML).
* XXX: An RNA sequence.
* YYY: A dot-bracket representation of this RNA.
* outFile: An output file whose format is guessed from the extension.
Many additional options are supported, matching the syntax of the Applet's parameters.
Namely, if param is a valid parameter for the VARNA Applet, then -param is an option
that has the exact same arguments and effects in the standalone, command-line version.
%%%%%%%%%%%%%%%%%%%%%% LEGAL STUFF AND USUAL DISCLAIMER %%%%%%%%%%%%%%%%%%%%%%%%%%
This file is part of VARNA version 3.1.
VARNA version 3.1 is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option) any
later version.
VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
VARNA version 3.1 (See LICENSE.txt file). If not, see http://www.gnu.org/licenses.
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