| 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. |