Package: wnpp Severity: wishlist * Package name : arb Version : 0.0.20041112 Upstream Author : Arb development team * URL : http://www.arb-home.de/ * License : Contains nonfree parts (see below) Description : [Biology] Integrated package for data handling and analysis
The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. The ARB project (latin, "arbor"=tree) is a joint initiative of the Lehrstuhl fuer Mikrobiologie <http://www.mikro.biologie.tu-muenchen.de/> and the Lehrstuhl fuer Rechnertechnik und Rechnerorganisation <http://wwwbode.informatik.tu-muenchen.de/> of the Technical University of Munich. Preliminary (and not yet fully working!) packages are available at http://people.debian.org/~tille/packages/arb/ Copyrights: ARB copyright and license information * 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. 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 Oliver Strunk, Ralf Westram & 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. * If you modify parts of ARB and redistribute these changes the 'Lehrstuhl fuer Mikrobiologie' gains the right to incorporate these changes into ARB and to redistribute them with future versions of ARB. 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. [Remark from the Debian package maintainer Andreas Tille] Phylp is not used in the binary package because the Debian package is used which is in the non-free part of Debian. Remark: After heavy discussion with the author of Phylip it was not possible to convince him to use a free license. 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 SPECIFICATION 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. [Remark from the Debian package maintainer Andreas Tille] I was unable to find a source URL where this program which is claimed as external can be downloaded. 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 authors 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 [Remark from the Debian package maintainer Andreas Tille] This is not used in the binary package because it is available as official Debian package named blast2 which is builded from the ncbi-tools6 source package and has a free license (see this package). CONVERT_ALN convert_aln -- an alignment(or sequence) converter written by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992. [Remark from the Debian package maintainer Andreas Tille] I was unable to find a source URL where this program which is claimed as external can be downloaded. TREETOOL * Written by Mike Maciukenas, at the RDP, with design and implementation guidance by Gary Olsen, Niels Larsen, Carl Woese. * Copyright (c) 1991, University of Illinois board of trustess. All rights reserved. * Treetool is a copyrighted program, not in the public domain. It is provided free of charge, and permission is granted to copy and dirstribute, provided that it is not done for profit, and that all copyright messages remain present and intact. [Remark from the Debian package maintainer Andreas Tille] This is not used in the binary package because the Debian package is used which is in the non-free part of Debian. Remark: It was not possible to contact the original author who stated that it would be planned to release the program under GPL but applied no license at all to the source package. 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. On Debian GNU/Linux systems you can find the text of this license under /usr/share/common-licenses/GPL * 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. * For any other enquiries write to Gary J. Olsen, Department of Microbiology, University of Illinois, Urbana, IL 61801, USA * Or send E-mail to [EMAIL PROTECTED] * 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: o Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376. o and o 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. [Remark from the Debian package maintainer Andreas Tille] This is not used in the binary package because it is available as official Debian package and has a free license (see this package). [Additions from the Debian package maintainer Andreas Tille] The source package also contains the external software packages treepuzzle: This is not used in the binary package because it is available as official Debian package and has a free license (see this package). readseq: This is not used in the binary package because it is available as official Debian package and has a free license (see this package). molphy: This is also not used in the binary package because the Debian package is used which is in the non-free part of Debian. Remark: The e-mail address of the author of this program was recently found and chances are not bad that the open license issues can be solved for this package. -- System Information: Debian Release: 3.1 APT prefers testing APT policy: (501, 'testing'), (50, 'unstable') Architecture: i386 (i686) Kernel: Linux 2.6.8 Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (ignored: LC_ALL set to [EMAIL PROTECTED])
