arb

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.

Packages

Thank you!