+++ /dev/null
-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.
projects / gentoo.git / commitdiff