ARB copyright and license information
The ARB software and documentation are not in the public domain.
External programs distributed together with ARB are copyrighted by and are the property of their respective authors unless otherwise stated.
All other copyrights are owned by Lehrstuhl fuer Mikrobiologie, TU Muenchen.
You have the right to use this version of ARB for free. Please read as well the attached copyright notices below whether you may or may not install this package.
Since many of the included programs is free software and nobody is allowed to sell that software you may safely assume ARB will never become a commercial product.
This release of the ARB program and documentation may not be sold or incorporated into a commercial product, in whole or in part, without the expressed written consent of the Technical University of Munich and of its supervisors Ralf Westram or Wolfgang Ludwig.
All interested parties may redistribute and modify ARB as long as all copies are accompanied by this license information and all copyright notices remain intact. Parties redistributing ARB must do so on a non-profit basis, charging only for cost of media or distribution.
If you modify parts of ARB and redistribute these changes the 'Lehrstuhl fuer Mikrobiologie' of the TU Muenchen gains the right to incorporate these changes into ARB and to redistribute them with future versions of ARB.
Some parts of arb are published under the ARB-public-library-license which should have been included in the file arb_PUBLIB_LICENSE.txt
That license explicitely allows the use of these parts of arb in GPL-licensed projects.
Hereby anybody is granted the right to build debian-pakets of the ARB software package (http:://www.arb-home.de/) and publish them on debian mirrors (or any other way of debian-distribution).
This includes any debian derivates like ubuntu.
The ARB developers may (but most likely wont ever) revoke this granting. If really done so, it'll only affect ARB versions released after such a revocation.
THE TU MUENCHEN AND THE VARIOUS AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. User understands the software is a research tool for which no warranties as to capabilities or accuracy are made, and user accepts the software "as is." User assumes the entire risk as to the results and performance of the software and documentation. The above parties cannot be held liable for any direct, indirect, consequential or incidental damages with respect to any claim by user or any third party on account of, or arising from the use of software and associated materials. This disclaimer covers both the ARB core applications and all external programs used by ARB.
Copyright notices for programs distributed together with ARB:
The Genetic Data Environment (GDE) software and documentation are not in the public domain. Portions of this code are owned and copyrighted by the The Board of Trustees of the University of Illinois and by Steven Smith. External functions used by GDE are the property of their authors. This release of the GDE program and documentation may not be sold, or incorporated into a commercial product, in whole or in part without the expressed written consent of the University of Illinois and of its author, Steven Smith.
All interested parties may redistribute the GDE as long as all copies are accompanied by this documentation, and all copyright notices remain intact. Parties interested in redistribution must do so on a non-profit basis, charging only for cost of media. Modifications to the GDE core editor should be forwarded to the author Steven Smith. External programs used by the GDE are copyrighted by, and are the property of their respective authors unless otherwise stated.
(c) Copyright 1986-1993 by Joseph Felsenstein and the University of Washington. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.
LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO PROXIMITY DATA
GEERT DE SOETE -- VERSION 1.01 - FEB. 1983
VERSION 1.02 - JUNE 1983
VERSION 1.03 - JULY 1983
´C´ version by Michael Macuikenas, University of Illinois
DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48, 621-626.
DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18, 387-393.
THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND SPECIFICATION OF MACHINE-DEPENDENT CONSTANTS. CF. FOX, P.A., HALL, A.D., & SCHRYER, N.L. THE PORT MATHEMATICAL SUBROUTINE LIBRAY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 104-126. ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.
UNIFORMLY DISTRIBUTED RANDOM NUMBERS ARE GENERATED BY A PROCEDURE DUE TO SCHRAGE. CF. SCHRAGE, L. A MORE PORTABLE FORTRAN RANDOM NUMBER GENERATOR. ACM TRANS. ON MATH. SOFTW., 1979, 5, 132-138.
SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE HARWELL SUBROUTINE LIBRARY (1979 EDITION).
ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE AUTHOR DISCLAIMS ANY RESPONSABILITY FOR POSSIBLE ERRORS.
| /* ===========================================================================
| * PUBLIC DOMAIN NOTICE
| * National Center for Biotechnology Information
| * This software/database is a "United States Government Work" under the
| * terms of the United States Copyright Act. It was written as part of
| * the author´s official duties as a United States Government employee and
| * thus cannot be copyrighted. This software/database is freely available
| * to the public for use. The National Library of Medicine and the U.S.
| * Government have not placed any restriction on its use or reproduction.
| * Although all reasonable efforts have been taken to ensure the accuracy
| * and reliability of the software and data, the NLM and the U.S.
| * Government do not and cannot warrant the performance or results that
| * may be obtained by using this software or data. The NLM and the U.S.
| * Government disclaim all warranties, express or implied, including
| * warranties of performance, merchantability or fitness for any particular
| * purpose.
| * Please cite the author in any work or product based on this material.
| * ===========================================================================*/
| Warren Gish
convert_aln -- an alignment(or sequence) converter written by Wen-Min Kuan
for the Ribosomal Database Project(RDP), April 28, 1992.
fastDNAml, a program for estimation of phylogenetic trees from sequences. Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
This program is free software; you may 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.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
For any other enquiries write to Gary J. Olsen, Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
Or send E-mail to firstname.lastname@example.org
fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
Copyright notice from dnaml:
version 3.3. (c) Copyright 1986, 1990 by the University of Washington and Joseph Felsenstein. Written by Joseph Felsenstein. Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed.
When publishing work that based on results from fastDNAml please cite:
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.
treepuzzle is published under the GPL (GNU GENERAL PUBLIC LICENSE) which is provided in 'lib/GPL.txt'.
Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
Copyright 1990 by d.g.gilbert biology dept., indiana university, bloomington, in 47405 e-mail: email@example.com
This program may be freely copied and used by anyone. Developers are encourged to incorporate parts in their programs, rather than devise their own private sequence format.
This should compile and run with any ANSI C compiler. Please advise me of any bugs, additions or corrections.
Copyright notices for headerlibs distributed together with ARB:
eigen is copyrighted by LGPL3 (copies are provided in HEADERLIBS/eigen.tgz)