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- Committer: Bazaar Package Importer
- Author(s): Andreas Tille
- Date: 2005-11-21 14:09:01 UTC
- Revision ID: james.westby@ubuntu.com-20051121140901-sck3ez9d6vvt66mk
Tags: 0.0.20050526-7
* arb-common recommends arb
* Added Build-Depends: g++
* Because there is no sign that this version shows the behaviour
reported in #325640 against the former version and the bug reporter
did not respond to any request I decide to close this bug. Feel
free to reopen if it seems necessary.
Clsoes: #325640
* Added Build-Depends: g++
* Because there is no sign that this version shows the behaviour
reported in #325640 against the former version and the bug reporter
did not respond to any request I decide to close this bug. Feel
free to reopen if it seems necessary.
Clsoes: #325640
- files added:
- config.makefile
- debian
- debian/bin
- debian/conf
- debian/po
- files modified:
- AWT/awt_canvas.hxx
added
removed
debian/copyright
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This package was debianized by Andreas Tille tille@debian.org on
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Thu, 3 Jun 2004 11:17:55 +0200.
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It was downloaded from
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http://www2.mikro.biologie.tu-muenchen.de/download/ARB/pre_release/
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The FTP archive where this version was downloaded from says:
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+---------------------------------------------------------------------------------+
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| |
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| IMPORTANT - Please read: |
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| |
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| The version in this directory is the latest build from our development team. |
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| Regard this version as 'NOT RELEASED'. |
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| |
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| You are DISALLOWED to supply copies of the files from this directory. |
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| As well you are DISALLOWED to make direct links to the files in this directory. |
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| |
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| Please do not encourage normal ARB users to download version from here. |
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| |
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| This version is completely untested and/or experimental - so it may easily |
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| VAPORIZE all your data, your machine or even yourself. |
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| |
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| |
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| *** Use at your own risk! *** |
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| |
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| |
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| The versions in the subdirectories below this directory are/have been used |
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| by several people at our institute, so they can be regarded as less dangerous |
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| than the latest build. |
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| |
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| Known bugs: |
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| |
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| - Many refresh problems in EDIT4 (2005_03_15 + 2005_03_31) |
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| - Secondary structure editor has problems with base positions |
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| (2005_03_15 + 2005_03_31 + 2005_05_06) |
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| |
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+---------------------------------------------------------------------------------+
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Ralf Westram, who is one of the authors below, wrote in private mail:
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> ------------------------------
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>
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> Hereby Andreas Tille is granted the right to build debian-pakets of
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> the ARB software http://www.arb-home.de/ and publish them on debian
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> mirrors.
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>
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> 1.9.2005
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> Ralf Westram <westram@arb-home.de>
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>
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> ------------------------------
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The authors are
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Department of Microbiology:
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Dr. Wolfgang Ludwig (Biologist) <ludwig@arb-home.de>
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Task: Group Leader; Inventor of ARB, knows everything about it
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Ralf Westram (Computer scientist) <westram@reallysoft.de>
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Task: General ARB development
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Dr. Lothar Richter (Biologist) <richter@arb-home.de>
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Task: ARB Database Curation and Automatization
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Arno Buchner (Biologist) <buchner@arb-home.de>
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Task: ARB Database Curation and Genomics
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Department of Computer Science:
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Prof. Dr. Thomas Ludwig (Computer Scientist) <thomas.ludwig@informatik.uni-heidelberg.de>
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Task: Computer Science Supervisor
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Dr. Harald Meier (Biologist) <meierh@arb-home.de>
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Task: ARB GENOME programming
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Gangolf Jobb (Biologist) <jobb@arb-home.de>
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Task: Development and integration of alignment- and tree-generation-software
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The homepage is
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http://www.arb-home.de/
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Copyrights:
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ARB copyright and license information
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* The ARB software and documentation are not in the public domain.
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* External programs distributed together with ARB are copyrighted
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by and are the property of their respective authors unless otherwise stated.
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* All other copyrights are owned by Lehrstuhl fuer Mikrobiologie, TU Muenchen.
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USAGE LICENSE
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You have the right to use this version of ARB for free. Please read as well the
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attached copyright notices below whether you may or may not install this package.
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REDISTRIBUTION LICENSE
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* This release of the ARB program and documentation may not be sold or
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incorporated into a commercial product, in whole or in part, without
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the expressed written consent of the Technical University of Munich and
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of its supervisors Oliver Strunk, Ralf Westram & Wolfgang Ludwig.
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* All interested parties may redistribute and modify ARB as long as all
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copies are accompanied by this license information and all copyright
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notices remain intact. Parties redistributing ARB must do so on a non-profit
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basis, charging only for cost of media.
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* If you modify parts of ARB and redistribute these changes the
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'Lehrstuhl fuer Mikrobiologie' gains the right to incorporate these changes
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into ARB and to redistribute them with future versions of ARB.
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Disclaimer
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THE TU MUENCHEN AND THE VARIOUS AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED
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OR IMPLIED FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT NOT
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LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR
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PURPOSE.
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User understands the software is a research tool for which no warranties as to
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capabilities or accuracy are made, and user accepts the software "as is."
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User assumes the entire risk as to the results and performance of the software
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and documentation. The above parties cannot be held liable for any direct,
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indirect, consequential or incidental damages with respect to any claim by user
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or any third party on account of, or arising from the use of software and
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associated materials. This disclaimer covers both the ARB core applications and
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all external programs used by ARB.
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Copyright notices for programs distributes together with ARB
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GDE
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* The Genetic Data Environment (GDE) software and documentation are not in the
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public domain. Portions of this code are owned and copyrighted by the
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The Board of Trustees of the University of Illinois and by Steven Smith.
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External functions used by GDE are the property of their authors.
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This release of the GDE program and documentation may not be sold, or
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incorporated into a commercial product, in whole or in part without the
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expressed written consent of the University of Illinois and of its author,
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Steven Smith.
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* All interested parties may redistribute the GDE as long as all copies are
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accompanied by this documentation, and all copyright notices remain intact.
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Parties interested in redistribution must do so on a non-profit basis,
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charging only for cost of media. Modifications to the GDE core editor
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should be forwarded to the author Steven Smith. External programs used
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by the GDE are copyrighted by, and are the property of their respective
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authors unless otherwise stated.
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PHYLIP
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(c) Copyright 1986-1993 by Joseph Felsenstein and the University of Washington.
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Permission is granted to copy this document provided that no fee is charged for
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it and that this copyright notice is not removed.
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[Remark from the Debian package maintainer Andreas Tille]
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Phylp is not used in the binary package because the Debian
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package is used which is in the non-free part of Debian.
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Remark: After heavy discussion with the author of Phylip it
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was not possible to convince him to use a free license.
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LSADT
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* LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO PROXIMITY DATA
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* GEERT DE SOETE -- VERSION 1.01 - FEB. 1983
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VERSION 1.02 - JUNE 1983
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VERSION 1.03 - JULY 1983
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* C version by Michael Macuikenas, University of Illinois
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* REFERENCE: DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
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ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48, 621-626.
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DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
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DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18, 387-393.
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* REMARKS *
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-----------
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1) THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR
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ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND SPECIFICATION
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OF MACHINE-DEPENDENT CONSTANTS.
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CF. FOX, P.A., HALL, A.D., & SCHRYER, N.L.
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THE PORT MATHEMATICAL SUBROUTINE LIBRAY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 104-126.
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ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.
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2) UNIFORMLY DISTRIBUTED RANDOM NUMBERS ARE GENERATED BY A PROCEDURE DUE
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TO SCHRAGE. CF. SCHRAGE, L. A MORE PORTABLE FORTRAN RANDOM NUMBER GENERATOR.
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ACM TRANS. ON MATH. SOFTW., 1979, 5, 132-138.
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3) SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE HARWELL SUBROUTINE
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LIBRARY (1979 EDITION).
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4) ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE AUTHOR DISCLAIMS
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ANY RESPONSABILITY FOR POSSIBLE ERRORS.
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[Remark from the Debian package maintainer Andreas Tille]
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I was unable to find a source URL where this program which is
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claimed as external can be downloaded.
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BLAST
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/* ===========================================================================
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*
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* PUBLIC DOMAIN NOTICE
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* National Center for Biotechnology Information
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*
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the authors official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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*
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* purpose.
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*
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* Please cite the author in any work or product based on this material.
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*
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* ===========================================================================*/
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Warren Gish
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NCBI/NLM
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[Remark from the Debian package maintainer Andreas Tille]
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This is not used in the binary package because it is available as
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official Debian package named blast2 which is builded from the
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ncbi-tools6 source package and has a free license (see this package).
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CONVERT_ALN
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convert_aln -- an alignment(or sequence) converter written by Wen-Min Kuan
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for the Ribsomal Database Project(RDP), April 28, 1992.
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[Remark from the Debian package maintainer Andreas Tille]
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I was unable to find a source URL where this program which is
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claimed as external can be downloaded.
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TREETOOL
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* Written by Mike Maciukenas, at the RDP, with design and implementation guidance by Gary Olsen, Niels Larsen, Carl Woese.
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* Copyright (c) 1991, University of Illinois board of trustess. All rights reserved.
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* 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.
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[Remark from the Debian package maintainer Andreas Tille]
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This is not used in the binary package because the Debian
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package is used which is in the non-free part of Debian.
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Remark: It was not possible to contact the original author who
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stated that it would be planned to release the program under GPL
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but applied no license at all to the source package.
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fastdnaml
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* fastDNAml, a program for estimation of phylogenetic trees from sequences.
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Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
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* This program is free software; you may redistribute it and/or modify it under
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the terms of the GNU General Public License as published by the Free Software
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Foundation; either version 2 of the License, or (at your option) any later
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version.
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On Debian GNU/Linux systems you can find the text of this license under
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/usr/share/common-licenses/GPL
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* This program is distributed in the hope that it will be useful, but
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WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
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more details.
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* For any other enquiries write to Gary J. Olsen, Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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* Or send E-mail to gary@phylo.life.uiuc.edu
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* fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
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* Copyright notice from dnaml:
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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.
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* When publishing work that based on results from fastDNAml please cite:
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o Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
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o and
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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.
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[Remark from the Debian package maintainer Andreas Tille]
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This is not used in the binary package because it is available as
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official Debian package and has a free license (see this package).
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[Additions from the Debian package maintainer Andreas Tille]
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The source package also contains the external software packages
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treepuzzle:
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This is not used in the binary package because it is available as
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official Debian package and has a free license (see this package).
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readseq:
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This is not used in the binary package because it is available as
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official Debian package and has a free license (see this package).
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molphy:
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This is also not used in the binary package because the Debian
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package is used which is in the non-free part of Debian.
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Remark: The e-mail address of the author of this program was
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recently found and chances are not bad that the open license
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issues can be solved for this package.
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Loggerhead is a web-based interface for Breezy
Version: 2.0.1