CGView

Copyright (C) 2004 Paul Stothard. This program 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 2 of the License, or (at your option) any later version. This program 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.

Citing CGView: Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.

ClustalW2

Licensing ClustalW and ClustalX Date:29 November 2007. The copyright for ClustalW and ClustalX is held by Des Higgins, Julie Thompson and Toby Gibson The binaries and source code are made available and can be distributed subject to the following conditions: Users are free to redistribute ClustalW or ClustalX in it's unmodified form as long as it is not for commercial gain. Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at gibson@embl.de If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at clustalw@ucd.ie where they will be considered for inclusion in future releases.

Frequently asked questions about Clustal licensing? ---------------------------------------------------
1. Do I have to pay to use ClustalW or ClustalX? No - unless you wish to redistribute Clustal for profit. In this case see question 4.
2. Can I redistribute the Clustal binaries and source code? Yes. We have always wanted to see Clustal have as wide a userbase and distribution network as possible and are happy to see other sites host copies of the official Clustal code.
3. Can I make changes to the source code? You can make changes for your own purposes but you should not redistribute the changed code.
4. I want to include ClustalW/ClustalX in a commercial application who should I contact? Toby Gibson at gibson@embl.de (also cc des.higgins@ucd.ie)
5. There is no Clustal distribution for platform X. I have changed the code in order to compile Clustal on this platform. Can I redistribute it? Ideally you should send us a copy of your source code changes as well as a binary. We will include it in our contributed binaries section on our FTP site along with an acknowledgement of your contribution.

Oligo Calc

Copyright Northwestern University, 1997-2009. This page may be freely linked or distributed for any educational or non-commercial use.

Citation:
Kibbe WA. 'OligoCalc: an online oligonucleotide properties calculator'. (2007) Nucleic Acids Res. 35(webserver issue): May 25. ( Abstract/Full text).

Primer3

Copyright (c) 1996,1997,1998,1999,2000,2001,2004 Whitehead Institute for Biomedical Research. 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 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. Redistributions of source code must also reproduce this information in the source code itself.
  2. If the program is modified, redistributions must include a notice (in the same places as above) indicating that the redistributed program is not identical to the version distributed by Whitehead Institute.
  3. All advertising materials mentioning features or use of this software must display the following acknowledgment:
    This product includes software developed by the Whitehead Institute for Biomedical Research.
  4. The name of the Whitehead Institute may not be used to endorse or promote products derived from this software without specific prior written permission.
We also request that use of this software be cited in publications as
Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386
Source code available at http://fokker.wi.mit.edu/primer3/.
THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE "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 WHITEHEAD INSTITUTE 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.

ReadSeq

Readseq by D.G. Gilbert, 2.1.26 (18-Oct-2007); Indiana University, Bloomington, Indiana
Software at http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

T-Coffee

© Centro de Regulacio Genomica and Cedric Notredame ( Thu Jul 23 21:59:17 WEST 2009).
GNU GENERAL PUBLIC LICENSE; Version 2, June 1991

Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.



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CGView  |  Primer3  |  ClustalW2  |  TCoffee  |  Oligo Calc  |  ReadSeq