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Revision 1.2 - (show annotations) (download)
Sat Nov 5 02:29:54 2011 UTC (2 years, 10 months ago) by ulm
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +15 -21 lines
Fix various licenses, encoding should be UTF-8, bug 389395.

1 Copyrights
2
3 ARB 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
77 Copyright 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 - 'C' 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 author's 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 Ribosomal Database Project(RDP), April 28, 1992.
183
184
185 fastdnaml
186
187 fastDNAml, a program for estimation of phylogenetic trees from
188 sequences. Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
189
190 This program is free software; you may redistribute it and/or
191 modify it under the terms of the GNU General Public License as
192 published by the Free Software Foundation; either version 2 of
193 the License, or (at your option) any later version.
194
195 This program is distributed in the hope that it will be
196 useful, but WITHOUT ANY WARRANTY; without even the implied
197 warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
198 PURPOSE. See the GNU General Public License for more details.
199
200 You should have received a copy of the GNU General Public License along
201 with this program; if not, write to the Free Software Foundation, Inc.,
202 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
203
204 For any other enquiries write to Gary J. Olsen, Department of
205 Microbiology, University of Illinois, Urbana, IL 61801, USA
206
207 Or send E-mail to gary@phylo.life.uiuc.edu
208
209 fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
210
211 Copyright notice from dnaml:
212
213 version 3.3. (c) Copyright 1986, 1990 by the University of
214 Washington and Joseph Felsenstein. Written by Joseph
215 Felsenstein. Permission is granted to copy and use this
216 program provided no fee is charged for it and provided
217 that this copyright notice is not removed.
218
219 When publishing work that based on results from fastDNAml please cite:
220
221 Felsenstein, J. 1981. Evolutionary trees from DNA
222 sequences: A maximum likelihood approach.
223 J. Mol. Evol. 17: 368-376.
224
225 and
226
227 Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R.
228 1994. fastDNAml: A tool for construction of phylogenetic
229 trees of DNA sequences using maximum likelihood.
230 Comput. Appl. Biosci. 10: 41-48.
231
232
233 treepuzzle
234
235 treepuzzle is published under the GPL (GNU GENERAL PUBLIC LICENSE)
236 which is provided in 'lib/GPL.txt'.
237
238 molphy
239
240 MOLPHY: A Computer Program Package for Molecular Phylogenetics
241
242 Readme
243 This is the MOLPHY (ProtML) distribution, version 2.3.
244 Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
245 All rights reserved.
246
247 MOLPHY is a program package for MOLecular PHYlogenetics.
248
249 ProtML is a main program in MOLPHY for inferring evolutionary trees from
250 PROTein (amino acid) sequences by using the Maximum Likelihood method.
251
252 Programs (C language)
253 ProtML: Maximum Likelihood Inference of Protein Phylogeny
254 NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
255 ProtST: Basic Statistics of Protein Sequences
256 NucST: Basic Statistics of Nucleic Acid Sequences
257 NJdist: Neighbor Joining Phylogeny from Distance Matrix
258 Utilities (Perl)
259 mollist: get identifiers list molrev: reverse DNA sequences
260 molcat: concatenate sequences molcut: get partial sequences
261 molmerge: merge sequences nuc2ptn: DNA -> Amino acid
262 rminsdel: remove INS/DEL sites molcodon: get specified codon sites
263 molinfo: get varied sites mol2mol: MOLPHY format beautifer
264 inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved
265 mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY
266 must2mol: MUST -> MOLPHY etc.
267
268 MOLPHY is a free software, and you can use and redistribute it.
269 The programs are written in a standard subset of C with UNIX-like OS.
270 The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS.
271 MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and
272 HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
273 However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.
274
275 NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available
276 by anonymous ftp in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/.
277
278 readseq
279
280
281 ReadSeq -- 1 Feb 93
282
283 Reads and writes nucleic/protein sequences in various
284 formats. Data files may have multiple sequences.
285
286 Copyright 1990 by d.g.gilbert
287 biology dept., indiana university, bloomington, in 47405
288 e-mail: gilbertd@bio.indiana.edu
289
290 This program may be freely copied and used by anyone.
291 Developers are encourged to incorporate parts in their
292 programs, rather than devise their own private sequence
293 format.
294
295 This should compile and run with any ANSI C compiler.
296 Please advise me of any bugs, additions or corrections.

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