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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.
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