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diff --git a/licenses/arb b/licenses/arb deleted file mode 100644 index b742625a8..000000000 --- a/licenses/arb +++ /dev/null @@ -1,296 +0,0 @@ -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. |