Remove use of Bio::Perl which has been moved to Bio-Procedural.

[bioperl-live.git] / LICENSE

BioPerl is licensed under the same terms as Perl itself, which means it is
dually-licensed under either the Artistic or GPL licenses.

Below are details of the Artistic License and, following it, the GPL.


                         The "Artistic License"

                                Preamble

The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some
semblance of artistic control over the development of the package,
while giving the users of the package the right to use and distribute
the Package in a more-or-less customary fashion, plus the right to make
reasonable modifications.

Definitions:

        "Package" refers to the collection of files distributed by the
        Copyright Holder, and derivatives of that collection of files
        created through textual modification.

        "Standard Version" refers to such a Package if it has not been
        modified, or has been modified in accordance with the wishes
        of the Copyright Holder as specified below.

        "Copyright Holder" is whoever is named in the copyright or
        copyrights for the package.

        "You" is you, if you're thinking about copying or distributing
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        "Reasonable copying fee" is whatever you can justify on the
        basis of media cost, duplication charges, time of people involved,
        and so on.  (You will not be required to justify it to the
        Copyright Holder, but only to the computing community at large
        as a market that must bear the fee.)

        "Freely Available" means that no fee is charged for the item
        itself, though there may be fees involved in handling the item.
        It also means that recipients of the item may redistribute it
        under the same conditions they received it.

1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that you
duplicate all of the original copyright notices and associated disclaimers.

2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder.  A Package
modified in such a way shall still be considered the Standard Version.

3. You may otherwise modify your copy of this Package in any way, provided
that you insert a prominent notice in each changed file stating how and
when you changed that file, and provided that you do at least ONE of the
following:

    a) place your modifications in the Public Domain or otherwise make them
    Freely Available, such as by posting said modifications to Usenet or
    an equivalent medium, or placing the modifications on a major archive
    site such as uunet.uu.net, or by allowing the Copyright Holder to include
    your modifications in the Standard Version of the Package.

    b) use the modified Package only within your corporation or organization.

    c) rename any non-standard executables so the names do not conflict
    with standard executables, which must also be provided, and provide
    a separate manual page for each non-standard executable that clearly
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    d) make other distribution arrangements with the Copyright Holder.

4. You may distribute the programs of this Package in object code or
executable form, provided that you do at least ONE of the following:

    a) distribute a Standard Version of the executables and library files,
    together with instructions (in the manual page or equivalent) on where
    to get the Standard Version.

    b) accompany the distribution with the machine-readable source of
    the Package with your modifications.

    c) give non-standard executables non-standard names, and clearly
    document the differences in manual pages (or equivalent), together
    with instructions on where to get the Standard Version.

    d) make other distribution arrangements with the Copyright Holder.

5. You may charge a reasonable copying fee for any distribution of this
Package.  You may charge any fee you choose for support of this
Package.  You may not charge a fee for this Package itself.  However,
you may distribute this Package in aggregate with other (possibly
commercial) programs as part of a larger (possibly commercial) software
distribution provided that you do not advertise this Package as a
product of your own.  You may embed this Package's interpreter within
an executable of yours (by linking); this shall be construed as a mere
form of aggregation, provided that the complete Standard Version of the
interpreter is so embedded.

6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall
under the copyright of this Package, but belong to whoever generated
them, and may be sold commercially, and may be aggregated with this
Package.  If such scripts or library files are aggregated with this
Package via the so-called "undump" or "unexec" methods of producing a
binary executable image, then distribution of such an image shall
neither be construed as a distribution of this Package nor shall it
fall under the restrictions of Paragraphs 3 and 4, provided that you do
not represent such an executable image as a Standard Version of this
Package.

7. C subroutines (or comparably compiled subroutines in other
languages) supplied by you and linked into this Package in order to
emulate subroutines and variables of the language defined by this
Package shall not be considered part of this Package, but are the
equivalent of input as in Paragraph 6, provided these subroutines do
not change the language in any way that would cause it to fail the
regression tests for the language.

8. Aggregation of this Package with a commercial distribution is always
permitted provided that the use of this Package is embedded; that is,
when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution.  Such use shall not be
construed as a distribution of this Package.

9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.

10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.

                                The End





GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
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not convey it at all.  For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.

  13. Use with the GNU Affero General Public License.

  Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work.  The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.

  14. Revised Versions of this License.

  The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time.  Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.

  Each version is given a distinguishing version number.  If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation.  If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.

  If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.

  Later license versions may give you additional or different
permissions.  However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.

  15. Disclaimer of Warranty.

  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

  16. Limitation of Liability.

  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.

  17. Interpretation of Sections 15 and 16.

  If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.

                     END OF TERMS AND CONDITIONS

            How to Apply These Terms to Your New Programs

  If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.

  To do so, attach the following notices to the program.  It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.

    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) <year>  <name of author>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 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, see <http://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

  If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:

    <program>  Copyright (C) <year>  <name of author>
    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    This is free software, and you are welcome to redistribute it
    under certain conditions; type `show c' for details.

The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License.  Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".

  You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.

  The GNU General Public License does not permit incorporating your program
into proprietary programs.  If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library.  If this is what you want to do, use the GNU Lesser General
Public License instead of this License.  But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.