source: tags/ms_r18q1/arb_LICENSE.txt

Last change on this file was 15365, checked in by westram, 5 years ago
  • allow use of selected parts of arb source in GPL licensed projects
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1Copyrights
2
3ARB copyright and license information
4
5    COPYRIGHTS
6
7        The ARB software and documentation are not in the public
8        domain.
9
10        External programs distributed together with ARB are
11        copyrighted by and are the property of their respective
12        authors unless otherwise stated.
13
14        All other copyrights are owned by Lehrstuhl fuer
15        Mikrobiologie, TU Muenchen.
16
17    USAGE LICENSE
18
19        You have the right to use this version of ARB for free.
20        Please read as well the attached copyright notices below
21        whether you may or may not install this package.
22
23        Since many of the included programs is free software and
24        nobody is allowed to sell that software you may safely assume
25        ARB will never become a commercial product.
26
27    REDISTRIBUTION LICENSE
28
29        This release of the ARB program and documentation may not be
30        sold or incorporated into a commercial product, in whole or in
31        part, without the expressed written consent of the Technical
32        University of Munich and of its supervisors Ralf Westram or
33        Wolfgang Ludwig.
34
35        All interested parties may redistribute and modify ARB as long
36        as all copies are accompanied by this license information and
37        all copyright notices remain intact.  Parties redistributing
38        ARB must do so on a non-profit basis, charging only for cost
39        of media or distribution.
40
41        If you modify parts of ARB and redistribute these changes the
42        'Lehrstuhl fuer Mikrobiologie' of the TU Muenchen gains the
43        right to incorporate these changes into ARB and to redistribute
44        them with future versions of ARB.
45
46    LIBRARY LICENSE
47
48        Some parts of arb are published under the ARB-public-library-license
49        which should have been included in the file arb_PUBLIB_LICENSE.txt
50
51        That license explicitely allows the use of these parts of arb
52        in GPL-licensed projects.
53
54    DEBIAN DISTRIBUTION
55
56        Hereby anybody is granted the right to build debian-pakets
57        of the ARB software package (http:://www.arb-home.de/) and
58        publish them on debian mirrors (or any other way of
59        debian-distribution).
60
61        This includes any debian derivates like ubuntu.
62
63        The ARB developers may (but most likely wont ever) revoke
64        this granting. If really done so, it'll only affect ARB
65        versions released after such a revocation.
66
67    DISCLAIMER
68
69        THE TU MUENCHEN AND THE VARIOUS AUTHORS OF ARB GIVE NO
70        WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND
71        DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY
72        OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR
73        PURPOSE.  User understands the software is a research tool for
74        which no warranties as to capabilities or accuracy are made,
75        and user accepts the software "as is." User assumes the entire
76        risk as to the results and performance of the software and
77        documentation. The above parties cannot be held liable for any
78        direct, indirect, consequential or incidental damages with
79        respect to any claim by user or any third party on account of,
80        or arising from the use of software and associated
81        materials. This disclaimer covers both the ARB core
82        applications and all external programs used by ARB.
83
84
85Copyright notices for programs distributed together with ARB:
86
87    GDE
88
89        The Genetic Data Environment (GDE) software and documentation
90        are not in the public domain. Portions of this code are owned
91        and copyrighted by the The Board of Trustees of the University
92        of Illinois and by Steven Smith. External functions used by
93        GDE are the property of their authors. This release of the GDE
94        program and documentation may not be sold, or incorporated
95        into a commercial product, in whole or in part without the
96        expressed written consent of the University of Illinois and of
97        its author, Steven Smith.
98
99        All interested parties may redistribute the GDE as long as all
100        copies are accompanied by this documentation, and all
101        copyright notices remain intact.  Parties interested in
102        redistribution must do so on a non-profit basis, charging only
103        for cost of media.  Modifications to the GDE core editor
104        should be forwarded to the author Steven Smith.  External
105        programs used by the GDE are copyrighted by, and are the
106        property of their respective authors unless otherwise stated.
107
108
109
110    PHYLIP
111
112        (c) Copyright 1986-1993 by Joseph Felsenstein and the
113        University of Washington. Permission is granted to copy this
114        document provided that no fee is charged for it and that this
115        copyright notice is not removed.
116
117    LSADT
118
119        LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO
120        PROXIMITY DATA
121
122                GEERT DE SOETE  --  VERSION 1.01 - FEB. 1983
123                                    VERSION 1.02 - JUNE 1983
124                                    VERSION 1.03 - JULY 1983
125
126                ŽCŽ version by Michael Macuikenas, University of Illinois
127
128        REFERENCE:
129
130                DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
131                ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48,
132                621-626.
133
134                DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
135                DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18,
136                387-393.
137
138        REMARKS
139
140          1. THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR
141             ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND
142             SPECIFICATION OF MACHINE-DEPENDENT CONSTANTS.
143             CF. FOX, P.A., HALL, A.D., & SCHRYER, N.L.
144             THE PORT MATHEMATICAL SUBROUTINE LIBRAY.
145             ACM TRANS. ON MATH. SOFTW., 1978, 4, 104-126.
146             ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY.
147             ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.
148   
149          2. UNIFORMLY DISTRIBUTED RANDOM NUMBERS ARE GENERATED BY A
150             PROCEDURE DUE TO SCHRAGE. CF.
151             SCHRAGE, L.  A MORE PORTABLE FORTRAN RANDOM NUMBER GENERATOR.
152             ACM TRANS. ON MATH. SOFTW., 1979, 5, 132-138.
153   
154          3. SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE
155             HARWELL SUBROUTINE LIBRARY (1979 EDITION).
156   
157          4. ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE
158             AUTHOR DISCLAIMS ANY RESPONSABILITY FOR POSSIBLE
159             ERRORS.
160
161    BLAST
162
163       | /* ===========================================================================
164       | *
165       | *                            PUBLIC DOMAIN NOTICE
166       | *               National Center for Biotechnology Information
167       | *
168       | *  This software/database is a "United States Government Work" under the
169       | *  terms of the United States Copyright Act.  It was written as part of
170       | *  the authorŽs official duties as a United States Government employee and
171       | *  thus cannot be copyrighted.  This software/database is freely available
172       | *  to the public for use. The National Library of Medicine and the U.S.
173       | *  Government have not placed any restriction on its use or reproduction.
174       | *
175       | *  Although all reasonable efforts have been taken to ensure the accuracy
176       | *  and reliability of the software and data, the NLM and the U.S.
177       | *  Government do not and cannot warrant the performance or results that
178       | *  may be obtained by using this software or data. The NLM and the U.S.
179       | *  Government disclaim all warranties, express or implied, including
180       | *  warranties of performance, merchantability or fitness for any particular
181       | *  purpose.
182       | *
183       | *  Please cite the author in any work or product based on this material.
184       | *
185       | * ===========================================================================*/
186       | Warren Gish
187       | NCBI/NLM
188
189    CONVERT_ALN
190
191        convert_aln --  an alignment(or sequence) converter written by Wen-Min Kuan
192                        for the Ribosomal Database Project(RDP), April 28, 1992.
193
194
195    fastdnaml
196
197        fastDNAml, a program for estimation of phylogenetic trees from
198        sequences. Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
199
200        This program is free software; you may redistribute it and/or
201        modify it under the terms of the GNU General Public License as
202        published by the Free Software Foundation; either version 2 of
203        the License, or (at your option) any later version.
204
205        This program is distributed in the hope that it will be
206        useful, but WITHOUT ANY WARRANTY; without even the implied
207        warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
208        PURPOSE.  See the GNU General Public License for more details.
209
210        You should have received a copy of the GNU General Public License along
211        with this program; if not, write to the Free Software Foundation, Inc.,
212        59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
213
214        For any other enquiries write to Gary J. Olsen, Department of
215        Microbiology, University of Illinois, Urbana, IL 61801, USA
216
217        Or send E-mail to gary@phylo.life.uiuc.edu
218
219        fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
220
221        Copyright notice from dnaml:
222
223            version 3.3. (c) Copyright 1986, 1990 by the University of
224            Washington and Joseph Felsenstein.  Written by Joseph
225            Felsenstein.  Permission is granted to copy and use this
226            program provided no fee is charged for it and provided
227            that this copyright notice is not removed.
228
229        When publishing work that based on results from fastDNAml please cite:
230
231            Felsenstein, J.  1981.  Evolutionary trees from DNA
232            sequences: A maximum likelihood approach.
233            J. Mol. Evol. 17: 368-376.
234
235            and
236
237            Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R.
238            1994.  fastDNAml: A tool for construction of phylogenetic
239            trees of DNA sequences using maximum likelihood.
240            Comput. Appl. Biosci. 10: 41-48.
241
242
243    treepuzzle
244
245        treepuzzle is published under the GPL (GNU GENERAL PUBLIC LICENSE)
246        which is provided in 'lib/GPL.txt'.
247
248    readseq
249
250
251         ReadSeq  -- 1 Feb 93
252         
253         Reads and writes nucleic/protein sequences in various
254         formats. Data files may have multiple sequences.
255         
256         Copyright 1990 by d.g.gilbert
257         biology dept., indiana university, bloomington, in 47405
258         e-mail: gilbertd@bio.indiana.edu
259         
260         This program may be freely copied and used by anyone.
261         Developers are encourged to incorporate parts in their
262         programs, rather than devise their own private sequence
263         format.
264         
265         This should compile and run with any ANSI C compiler.
266         Please advise me of any bugs, additions or corrections.
267
268
269Copyright notices for headerlibs distributed together with ARB:
270
271     eigen (2.0.16)
272
273        eigen is copyrighted by LGPL3
274        (copies are provided in HEADERLIBS/eigen.tgz)
275
276
277
278
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