source: branches/profile/arb_LICENSE.txt

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