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diff --git a/licenses/arb b/licenses/arb new file mode 100644 index 000000000..b742625a8 --- /dev/null +++ b/licenses/arb @@ -0,0 +1,296 @@ +Copyrights + +ARB copyright and license information + + COPYRIGHTS + + The ARB software and documentation are not in the public + domain. + + 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 + debian-distribution). + + 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. + + DISCLAIMER + + 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 + + GDE + + 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. + + + + PHYLIP + + (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. + + LSADT + + 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, + 621-626. + DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE + DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18, + 387-393. + + - 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 + ERRORS. + + BLAST + + /* =========================================================================== + * + * 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 + NCBI/NLM + + CONVERT_ALN + + convert_aln -- an alignment(or sequence) converter written by Wen-Min Kuan + for the Ribosomal Database Project(RDP), April 28, 1992. + + + fastdnaml + + 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 gary@phylo.life.uiuc.edu + + 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. + + and + + 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 + + treepuzzle is published under the GPL (GNU GENERAL PUBLIC LICENSE) + which is provided in 'lib/GPL.txt'. + + molphy + + MOLPHY: A Computer Program Package for Molecular Phylogenetics + + Readme + 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 + + + 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: gilbertd@bio.indiana.edu + + 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 + format. + + This should compile and run with any ANSI C compiler. + Please advise me of any bugs, additions or corrections. |