source: tags/cvs_2_svn/arb_LICENSE.txt

Last change on this file was 5431, checked in by westram, 16 years ago
  • grant rights for debian distributions
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 13.2 KB
Line 
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 distributes 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: DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
121           ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48,
122           621-626.
123           DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
124           DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18,
125           387-393.
126
127      - REMARKS
128
129            ------
130
131        1) THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR
132           ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND SPECIFICA-
133           TION OF MACHINE-DEPENDENT CONSTANTS.
134           CF. FOX, P.A., HALL, A.D., & SCHRYER, N.L.
135
136            THE PORT MATHEMATICAL SUBROUTINE LIBRAY. ACM TRANS. ON MATH.
137            SOFTW., 1978, 4, 104-126.
138
139                 ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY.
140                 ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.
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        3) SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE
146           HARWELL SUBROUTINE LIBRARY (1979 EDITION).
147        4) ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE
148           AUTHOR DISCLAIMS ANY RESPONSABILITY FOR POSSIBLE
149           ERRORS.
150
151    BLAST
152
153        /* ===========================================================================
154        *
155        *                            PUBLIC DOMAIN NOTICE
156        *               National Center for Biotechnology Information
157        *
158        *  This software/database is a "United States Government Work" under the
159        *  terms of the United States Copyright Act.  It was written as part of
160        *  the authorŽs official duties as a United States Government employee and
161        *  thus cannot be copyrighted.  This software/database is freely available
162        *  to the public for use. The National Library of Medicine and the U.S.
163        *  Government have not placed any restriction on its use or reproduction.
164        *
165        *  Although all reasonable efforts have been taken to ensure the accuracy
166        *  and reliability of the software and data, the NLM and the U.S.
167        *  Government do not and cannot warrant the performance or results that
168        *  may be obtained by using this software or data. The NLM and the U.S.
169        *  Government disclaim all warranties, express or implied, including
170        *  warranties of performance, merchantability or fitness for any particular
171        *  purpose.
172        *
173        *  Please cite the author in any work or product based on this material.
174        *
175        * ===========================================================================*/
176        Warren Gish
177        NCBI/NLM
178
179    CONVERT_ALN
180
181        convert_aln --  an alignment(or sequence) converter written by Wen-Min Kuan
182                        for the Ribsomal Database Project(RDP), April 28, 1992.
183
184
185
186    TREETOOL
187
188        Written by Mike Maciukenas, at the RDP, with design and
189        implementation guidance by Gary Olsen, Niels Larsen, Carl
190        Woese.
191
192        Copyright (c) 1991, University of Illinois board of
193        trustess. All rights reserved.
194
195        Treetool is a copyrighted program, not in the public
196        domain. It is provided free of charge, and permission is
197        granted to copy and dirstribute, provided that it is not done
198        for profit, and that all copyright messages remain present and
199        intact.
200
201
202    fastdnaml
203
204        fastDNAml, a program for estimation of phylogenetic trees from
205        sequences. Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
206
207        This program is free software; you may redistribute it and/or
208        modify it under the terms of the GNU General Public License as
209        published by the Free Software Foundation; either version 2 of
210        the License, or (at your option) any later version.
211
212        This program is distributed in the hope that it will be
213        useful, but WITHOUT ANY WARRANTY; without even the implied
214        warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
215        PURPOSE.  See the GNU General Public License for more details.
216
217        You should have received a copy of the GNU General Public License along
218        with this program; if not, write to the Free Software Foundation, Inc.,
219        59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
220
221        For any other enquiries write to Gary J. Olsen, Department of
222        Microbiology, University of Illinois, Urbana, IL 61801, USA
223
224        Or send E-mail to gary@phylo.life.uiuc.edu
225
226        fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
227
228        Copyright notice from dnaml:
229
230            version 3.3. (c) Copyright 1986, 1990 by the University of
231            Washington and Joseph Felsenstein.  Written by Joseph
232            Felsenstein.  Permission is granted to copy and use this
233            program provided no fee is charged for it and provided
234            that this copyright notice is not removed.
235
236        When publishing work that based on results from fastDNAml please cite:
237
238            Felsenstein, J.  1981.  Evolutionary trees from DNA
239            sequences: A maximum likelihood approach.
240            J. Mol. Evol. 17: 368-376.
241
242            and
243
244            Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R.
245            1994.  fastDNAml: A tool for construction of phylogenetic
246            trees of DNA sequences using maximum likelihood.
247            Comput. Appl. Biosci. 10: 41-48.
248
249
250    treepuzzle
251
252        treepuzzle is published under the GPL (GNU GENERAL PUBLIC LICENSE)
253        which is provided in 'lib/GPL.txt'.
254
255    molphy
256
257        MOLPHY: A Computer Program Package for Molecular Phylogenetics
258       
259        Readme
260               This is the MOLPHY (ProtML) distribution,  version 2.3.
261                Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
262                                 All rights reserved.
263       
264                MOLPHY is a program package for MOLecular PHYlogenetics.
265       
266        ProtML is a main program in MOLPHY for inferring evolutionary trees from
267        PROTein (amino acid) sequences by using the Maximum Likelihood method.
268       
269        Programs (C language)
270          ProtML: Maximum Likelihood Inference of Protein Phylogeny
271          NucML:  Maximum Likelihood Inference of Nucleic Acid Phylogeny
272          ProtST: Basic Statistics of Protein Sequences
273          NucST:  Basic Statistics of Nucleic Acid Sequences
274          NJdist: Neighbor Joining Phylogeny from Distance Matrix
275        Utilities (Perl)
276          mollist:  get identifiers list        molrev:   reverse DNA sequences
277          molcat:   concatenate sequences       molcut:   get partial sequences
278          molmerge: merge sequences             nuc2ptn:  DNA -> Amino acid
279          rminsdel: remove INS/DEL sites        molcodon: get specified codon sites
280          molinfo:  get varied sites            mol2mol:  MOLPHY format beautifer
281          inl2mol:  Interleaved -> MOLPHY       mol2inl:  MOLPHY -> Interleaved
282          mol2phy:  MOLPHY -> Sequential        phy2mol:  Sequential -> MOLPHY
283          must2mol: MUST -> MOLPHY              etc.
284       
285        MOLPHY is a free software, and you can use and redistribute it.
286        The programs are written in a standard subset of C with UNIX-like OS.
287        The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS.
288        MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and
289        HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
290        However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.
291       
292        NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available
293        by anonymous ftp in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/.
294
295    readseq
296
297
298         ReadSeq  -- 1 Feb 93
299         
300         Reads and writes nucleic/protein sequences in various
301         formats. Data files may have multiple sequences.
302         
303         Copyright 1990 by d.g.gilbert
304         biology dept., indiana university, bloomington, in 47405
305         e-mail: gilbertd@bio.indiana.edu
306         
307         This program may be freely copied and used by anyone.
308         Developers are encourged to incorporate parts in their
309         programs, rather than devise their own private sequence
310         format.
311         
312         This should compile and run with any ANSI C compiler.
313         Please advise me of any bugs, additions or corrections.
314
315
316
317
318
319
Note: See TracBrowser for help on using the repository browser.