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297 lines
12 KiB
297 lines
12 KiB
Copyrights
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ARB copyright and license information
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COPYRIGHTS
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The ARB software and documentation are not in the public
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domain.
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External programs distributed together with ARB are
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copyrighted by and are the property of their respective
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authors unless otherwise stated.
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All other copyrights are owned by Lehrstuhl fuer
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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.
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Please read as well the attached copyright notices below
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whether you may or may not install this package.
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Since many of the included programs is free software and
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nobody is allowed to sell that software you may safely assume
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ARB will never become a commercial product.
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REDISTRIBUTION LICENSE
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This release of the ARB program and documentation may not be
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sold or incorporated into a commercial product, in whole or in
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part, without the expressed written consent of the Technical
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University of Munich and of its supervisors Ralf Westram or
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Wolfgang Ludwig.
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All interested parties may redistribute and modify ARB as long
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as all copies are accompanied by this license information and
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all copyright notices remain intact. Parties redistributing
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ARB must do so on a non-profit basis, charging only for cost
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of media or distribution.
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If you modify parts of ARB and redistribute these changes the
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'Lehrstuhl fuer Mikrobiologie' of the TU Muenchen gains the
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right to incorporate these changes into ARB and to redistribute
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them with future versions of ARB.
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DEBIAN DISTRIBUTION
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Hereby anybody is granted the right to build debian-pakets
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of the ARB software package (http:://www.arb-home.de/) and
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publish them on debian mirrors (or any other way of
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debian-distribution).
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This includes any debian derivates like ubuntu.
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The ARB developers may (but most likely wont ever) revoke
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this granting. If really done so, it'll only affect ARB
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versions released after such a revocation.
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DISCLAIMER
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THE TU MUENCHEN AND THE VARIOUS AUTHORS OF ARB GIVE NO
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WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND
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DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY
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OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR
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PURPOSE. User understands the software is a research tool for
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which no warranties as to capabilities or accuracy are made,
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and user accepts the software "as is." User assumes the entire
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risk as to the results and performance of the software and
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documentation. The above parties cannot be held liable for any
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direct, indirect, consequential or incidental damages with
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respect to any claim by user or any third party on account of,
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or arising from the use of software and associated
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materials. This disclaimer covers both the ARB core
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applications and 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
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are not in the public domain. Portions of this code are owned
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and copyrighted by the The Board of Trustees of the University
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of Illinois and by Steven Smith. External functions used by
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GDE are the property of their authors. This release of the GDE
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program and documentation may not be sold, or incorporated
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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
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its author, Steven Smith.
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All interested parties may redistribute the GDE as long as all
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copies are accompanied by this documentation, and all
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copyright notices remain intact. Parties interested in
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redistribution must do so on a non-profit basis, charging only
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for cost of media. Modifications to the GDE core editor
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should be forwarded to the author Steven Smith. External
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programs used by the GDE are copyrighted by, and are the
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property of their respective authors unless otherwise stated.
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PHYLIP
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(c) Copyright 1986-1993 by Joseph Felsenstein and the
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University of Washington. Permission is granted to copy this
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document provided that no fee is charged for it and that this
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copyright notice is not removed.
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LSADT
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LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO
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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,
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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,
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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 SPECIFICA-
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TION 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.
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SOFTW., 1978, 4, 104-126.
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ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY.
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ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.
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2) UNIFORMLY DISTRIBUTED RANDOM NUMBERS ARE GENERATED BY A
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PROCEDURE DUE TO SCHRAGE. CF.
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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
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HARWELL SUBROUTINE LIBRARY (1979 EDITION).
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4) ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE
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AUTHOR DISCLAIMS ANY RESPONSABILITY FOR POSSIBLE
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ERRORS.
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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 author's 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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CONVERT_ALN
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convert_aln -- an alignment(or sequence) converter written by Wen-Min Kuan
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for the Ribosomal Database Project(RDP), April 28, 1992.
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fastdnaml
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fastDNAml, a program for estimation of phylogenetic trees from
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sequences. Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
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This program is free software; you may redistribute it and/or
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modify it under the terms of the GNU General Public License as
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published by the Free Software Foundation; either version 2 of
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the License, or (at your option) any later version.
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This program is distributed in the hope that it will be
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useful, but WITHOUT ANY WARRANTY; without even the implied
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warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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PURPOSE. See the GNU General Public License for more details.
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You should have received a copy of the GNU General Public License along
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with this program; if not, write to the Free Software Foundation, Inc.,
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59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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For any other enquiries write to Gary J. Olsen, Department of
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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
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Washington and Joseph Felsenstein. Written by Joseph
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Felsenstein. Permission is granted to copy and use this
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program provided no fee is charged for it and provided
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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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Felsenstein, J. 1981. Evolutionary trees from DNA
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sequences: A maximum likelihood approach.
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J. Mol. Evol. 17: 368-376.
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and
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Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R.
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1994. fastDNAml: A tool for construction of phylogenetic
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trees of DNA sequences using maximum likelihood.
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Comput. Appl. Biosci. 10: 41-48.
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treepuzzle
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treepuzzle is published under the GPL (GNU GENERAL PUBLIC LICENSE)
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which is provided in 'lib/GPL.txt'.
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molphy
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MOLPHY: A Computer Program Package for Molecular Phylogenetics
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Readme
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This is the MOLPHY (ProtML) distribution, version 2.3.
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Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
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All rights reserved.
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MOLPHY is a program package for MOLecular PHYlogenetics.
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ProtML is a main program in MOLPHY for inferring evolutionary trees from
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PROTein (amino acid) sequences by using the Maximum Likelihood method.
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Programs (C language)
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ProtML: Maximum Likelihood Inference of Protein Phylogeny
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NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
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ProtST: Basic Statistics of Protein Sequences
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NucST: Basic Statistics of Nucleic Acid Sequences
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NJdist: Neighbor Joining Phylogeny from Distance Matrix
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Utilities (Perl)
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mollist: get identifiers list molrev: reverse DNA sequences
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molcat: concatenate sequences molcut: get partial sequences
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molmerge: merge sequences nuc2ptn: DNA -> Amino acid
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rminsdel: remove INS/DEL sites molcodon: get specified codon sites
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molinfo: get varied sites mol2mol: MOLPHY format beautifer
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inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved
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mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY
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must2mol: MUST -> MOLPHY etc.
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MOLPHY is a free software, and you can use and redistribute it.
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The programs are written in a standard subset of C with UNIX-like OS.
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The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS.
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MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and
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HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
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However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.
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NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available
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by anonymous ftp in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/.
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readseq
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ReadSeq -- 1 Feb 93
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Reads and writes nucleic/protein sequences in various
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formats. Data files may have multiple sequences.
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Copyright 1990 by d.g.gilbert
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biology dept., indiana university, bloomington, in 47405
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e-mail: gilbertd@bio.indiana.edu
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This program may be freely copied and used by anyone.
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Developers are encourged to incorporate parts in their
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programs, rather than devise their own private sequence
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format.
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This should compile and run with any ANSI C compiler.
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Please advise me of any bugs, additions or corrections.
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