Diffstat (limited to 'licenses/arb')
1 files changed, 296 insertions, 0 deletions
diff --git a/licenses/arb b/licenses/arb
new file mode 100644
@@ -0,0 +1,296 @@
+ARB copyright and license information
+ The ARB software and documentation are not in the public
+ 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.
+ USAGE LICENSE
+ 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.
+ REDISTRIBUTION LICENSE
+ 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.
+ DEBIAN DISTRIBUTION
+ 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
+ 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 distributes 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
+ REFERENCE: DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
+ ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48,
+ DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
+ DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18,
+ - REMARKS
+ 1) THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR
+ ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND SPECIFICA-
+ TION 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.
+ 2) 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.
+ 3) SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE
+ HARWELL SUBROUTINE LIBRARY (1979 EDITION).
+ 4) ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE
+ AUTHOR DISCLAIMS ANY RESPONSABILITY FOR POSSIBLE
+ /* ===========================================================================
+ * 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'.
+ MOLPHY: A Computer Program Package for Molecular Phylogenetics
+ This is the MOLPHY (ProtML) distribution, version 2.3.
+ Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
+ All rights reserved.
+ MOLPHY is a program package for MOLecular PHYlogenetics.
+ ProtML is a main program in MOLPHY for inferring evolutionary trees from
+ PROTein (amino acid) sequences by using the Maximum Likelihood method.
+ Programs (C language)
+ ProtML: Maximum Likelihood Inference of Protein Phylogeny
+ NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
+ ProtST: Basic Statistics of Protein Sequences
+ NucST: Basic Statistics of Nucleic Acid Sequences
+ NJdist: Neighbor Joining Phylogeny from Distance Matrix
+ Utilities (Perl)
+ mollist: get identifiers list molrev: reverse DNA sequences
+ molcat: concatenate sequences molcut: get partial sequences
+ molmerge: merge sequences nuc2ptn: DNA -> Amino acid
+ rminsdel: remove INS/DEL sites molcodon: get specified codon sites
+ molinfo: get varied sites mol2mol: MOLPHY format beautifer
+ inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved
+ mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY
+ must2mol: MUST -> MOLPHY etc.
+ MOLPHY is a free software, and you can use and redistribute it.
+ The programs are written in a standard subset of C with UNIX-like OS.
+ The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS.
+ MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and
+ HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
+ However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.
+ NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available
+ by anonymous ftp in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/.
+ ReadSeq -- 1 Feb 93
+ 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
+ This should compile and run with any ANSI C compiler.
+ Please advise me of any bugs, additions or corrections.