**WARNING**: some parts of the repository are *NOT* open-source. these are

copyright their respective owners.

the open-source parts of the repository are licensed as described in _license/.

**IMPORTANT**: when redistributing, it recommended to include _license/, so that

the open-source proof is included along with the license text.

the repository as a whole, *EXCEPT* the non-open-source parts, is collectively

licensed under the following terms (GPL2+):

-----

BIEN 3

Copyright (C) 2014  The Regents of the University of California, The Arizona

Board of Regents, Ecological Society of America

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 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.,

51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

-----

                    GNU GENERAL PUBLIC LICENSE

                       Version 2, June 1991

 Copyright (C) 1989, 1991 Free Software Foundation, Inc.,

 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

 Everyone is permitted to copy and distribute verbatim copies

 of this license document, but changing it is not allowed.

                            Preamble

  The licenses for most software are designed to take away your

freedom to share and change it.  By contrast, the GNU General Public

License is intended to guarantee your freedom to share and change free

software--to make sure the software is free for all its users.  This

General Public License applies to most of the Free Software

Foundation's software and to any other program whose authors commit to

using it.  (Some other Free Software Foundation software is covered by

the GNU Lesser General Public License instead.)  You can apply it to

your programs, too.

  When we speak of free software, we are referring to freedom, not

price.  Our General Public Licenses are designed to make sure that you

have the freedom to distribute copies of free software (and charge for

this service if you wish), that you receive source code or can get it

if you want it, that you can change the software or use pieces of it

in new free programs; and that you know you can do these things.

  To protect your rights, we need to make restrictions that forbid

anyone to deny you these rights or to ask you to surrender the rights.

These restrictions translate to certain responsibilities for you if you

distribute copies of the software, or if you modify it.

  For example, if you distribute copies of such a program, whether

gratis or for a fee, you must give the recipients all the rights that

you have.  You must make sure that they, too, receive or can get the

source code.  And you must show them these terms so they know their

rights.

  We protect your rights with two steps: (1) copyright the software, and

(2) offer you this license which gives you legal permission to copy,

distribute and/or modify the software.

  Also, for each author's protection and ours, we want to make certain

that everyone understands that there is no warranty for this free

software.  If the software is modified by someone else and passed on, we

want its recipients to know that what they have is not the original, so

that any problems introduced by others will not reflect on the original

authors' reputations.

  Finally, any free program is threatened constantly by software

patents.  We wish to avoid the danger that redistributors of a free

program will individually obtain patent licenses, in effect making the

program proprietary.  To prevent this, we have made it clear that any

patent must be licensed for everyone's free use or not licensed at all.

  The precise terms and conditions for copying, distribution and

modification follow.

                    GNU GENERAL PUBLIC LICENSE

   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

  0. This License applies to any program or other work which contains

a notice placed by the copyright holder saying it may be distributed

under the terms of this General Public License.  The "Program", below,

refers to any such program or work, and a "work based on the Program"

means either the Program or any derivative work under copyright law:

that is to say, a work containing the Program or a portion of it,

either verbatim or with modifications and/or translated into another

language.  (Hereinafter, translation is included without limitation in

the term "modification".)  Each licensee is addressed as "you".

Activities other than copying, distribution and modification are not

covered by this License; they are outside its scope.  The act of

running the Program is not restricted, and the output from the Program

is covered only if its contents constitute a work based on the

Program (independent of having been made by running the Program).

Whether that is true depends on what the Program does.

  1. You may copy and distribute verbatim copies of the Program's

source code as you receive it, in any medium, provided that you

conspicuously and appropriately publish on each copy an appropriate

copyright notice and disclaimer of warranty; keep intact all the

notices that refer to this License and to the absence of any warranty;

and give any other recipients of the Program a copy of this License

along with the Program.

You may charge a fee for the physical act of transferring a copy, and

you may at your option offer warranty protection in exchange for a fee.

  2. You may modify your copy or copies of the Program or any portion

of it, thus forming a work based on the Program, and copy and

distribute such modifications or work under the terms of Section 1

above, provided that you also meet all of these conditions:

    a) You must cause the modified files to carry prominent notices

    stating that you changed the files and the date of any change.

    b) You must cause any work that you distribute or publish, that in

    whole or in part contains or is derived from the Program or any

    part thereof, to be licensed as a whole at no charge to all third

    parties under the terms of this License.

    c) If the modified program normally reads commands interactively

    when run, you must cause it, when started running for such

    interactive use in the most ordinary way, to print or display an

    announcement including an appropriate copyright notice and a

    notice that there is no warranty (or else, saying that you provide

    a warranty) and that users may redistribute the program under

    these conditions, and telling the user how to view a copy of this

    License.  (Exception: if the Program itself is interactive but

    does not normally print such an announcement, your work based on

    the Program is not required to print an announcement.)

These requirements apply to the modified work as a whole.  If

identifiable sections of that work are not derived from the Program,

and can be reasonably considered independent and separate works in

themselves, then this License, and its terms, do not apply to those

sections when you distribute them as separate works.  But when you

distribute the same sections as part of a whole which is a work based

on the Program, the distribution of the whole must be on the terms of

this License, whose permissions for other licensees extend to the

entire whole, and thus to each and every part regardless of who wrote it.

Thus, it is not the intent of this section to claim rights or contest

your rights to work written entirely by you; rather, the intent is to

exercise the right to control the distribution of derivative or

collective works based on the Program.

In addition, mere aggregation of another work not based on the Program

with the Program (or with a work based on the Program) on a volume of

a storage or distribution medium does not bring the other work under

the scope of this License.

  3. You may copy and distribute the Program (or a work based on it,

under Section 2) in object code or executable form under the terms of

Sections 1 and 2 above provided that you also do one of the following:

    a) Accompany it with the complete corresponding machine-readable

    source code, which must be distributed under the terms of Sections

    1 and 2 above on a medium customarily used for software interchange; or,

    b) Accompany it with a written offer, valid for at least three

    years, to give any third party, for a charge no more than your

    cost of physically performing source distribution, a complete

    machine-readable copy of the corresponding source code, to be

    distributed under the terms of Sections 1 and 2 above on a medium

    customarily used for software interchange; or,

    c) Accompany it with the information you received as to the offer

    to distribute corresponding source code.  (This alternative is

    allowed only for noncommercial distribution and only if you

    received the program in object code or executable form with such

    an offer, in accord with Subsection b above.)

The source code for a work means the preferred form of the work for

making modifications to it.  For an executable work, complete source

code means all the source code for all modules it contains, plus any

associated interface definition files, plus the scripts used to

control compilation and installation of the executable.  However, as a

special exception, the source code distributed need not include

anything that is normally distributed (in either source or binary

form) with the major components (compiler, kernel, and so on) of the

operating system on which the executable runs, unless that component

itself accompanies the executable.

If distribution of executable or object code is made by offering

access to copy from a designated place, then offering equivalent

access to copy the source code from the same place counts as

distribution of the source code, even though third parties are not

compelled to copy the source along with the object code.

  4. You may not copy, modify, sublicense, or distribute the Program

except as expressly provided under this License.  Any attempt

otherwise to copy, modify, sublicense or distribute the Program is

void, and will automatically terminate your rights under this License.

However, parties who have received copies, or rights, from you under

this License will not have their licenses terminated so long as such

parties remain in full compliance.

  5. You are not required to accept this License, since you have not

signed it.  However, nothing else grants you permission to modify or

distribute the Program or its derivative works.  These actions are

prohibited by law if you do not accept this License.  Therefore, by

modifying or distributing the Program (or any work based on the

Program), you indicate your acceptance of this License to do so, and

all its terms and conditions for copying, distributing or modifying

the Program or works based on it.

  6. Each time you redistribute the Program (or any work based on the

Program), the recipient automatically receives a license from the

original licensor to copy, distribute or modify the Program subject to

these terms and conditions.  You may not impose any further

restrictions on the recipients' exercise of the rights granted herein.

You are not responsible for enforcing compliance by third parties to

this License.

  7. If, as a consequence of a court judgment or allegation of patent

infringement or for any other reason (not limited to patent issues),

conditions are imposed on you (whether by court order, agreement or

otherwise) that contradict the conditions of this License, they do not

excuse you from the conditions of this License.  If you cannot

distribute so as to satisfy simultaneously your obligations under this

License and any other pertinent obligations, then as a consequence you

may not distribute the Program at all.  For example, if a patent

license would not permit royalty-free redistribution of the Program by

all those who receive copies directly or indirectly through you, then

the only way you could satisfy both it and this License would be to

refrain entirely from distribution of the Program.

If any portion of this section is held invalid or unenforceable under

any particular circumstance, the balance of the section is intended to

apply and the section as a whole is intended to apply in other

circumstances.

It is not the purpose of this section to induce you to infringe any

patents or other property right claims or to contest validity of any

such claims; this section has the sole purpose of protecting the

integrity of the free software distribution system, which is

implemented by public license practices.  Many people have made

generous contributions to the wide range of software distributed

through that system in reliance on consistent application of that

system; it is up to the author/donor to decide if he or she is willing

to distribute software through any other system and a licensee cannot

impose that choice.

This section is intended to make thoroughly clear what is believed to

be a consequence of the rest of this License.

  8. If the distribution and/or use of the Program is restricted in

certain countries either by patents or by copyrighted interfaces, the

original copyright holder who places the Program under this License

may add an explicit geographical distribution limitation excluding

those countries, so that distribution is permitted only in or among

countries not thus excluded.  In such case, this License incorporates

the limitation as if written in the body of this License.

  9. The Free Software Foundation may publish revised and/or new versions

of the 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 a version number of this License which applies to it and "any

later version", you have the option of following the terms and conditions

either of that version or of any later version published by the Free

Software Foundation.  If the Program does not specify a version number of

this License, you may choose any version ever published by the Free Software

Foundation.

  10. If you wish to incorporate parts of the Program into other free

programs whose distribution conditions are different, write to the author

to ask for permission.  For software which is copyrighted by the Free

Software Foundation, write to the Free Software Foundation; we sometimes

make exceptions for this.  Our decision will be guided by the two goals

of preserving the free status of all derivatives of our free software and

of promoting the sharing and reuse of software generally.

                            NO WARRANTY

  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, 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.

  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING

WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR

REDISTRIBUTE 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.

                     END OF TERMS AND CONDITIONS

-----

Copyright (c) 2013, The Regents of the University of California

All rights reserved.

Redistribution and use in source and binary forms, with or without modification,

are permitted provided that the following conditions are met:

1.	Redistributions of source code must retain the above copyright notice, this

	list of conditions and the following disclaimer.

2.	Redistributions in binary form must reproduce the above copyright notice,

	this list of conditions and the following disclaimer in the documentation

	and/or other materials provided with the distribution.

3.	Neither the name of the copyright holder nor the names of its contributors

	may be used to endorse or promote products derived from this software

	without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND

ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR

ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES

(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON

ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

-----

Copyright 2013. The Arizona Board of Regents on behalf of The University of

Arizona. All rights reserved.

Program developed by: iPlant Collaborative as a collaboration between

participants at BIO5 at The University of Arizona (the primary hosting

institution), Cold Spring Harbor Laboratory, The University of Texas at Austin,

The University of North Carolina at Wilmington and individual contributors. Find

out more at http://www.iplantcollaborative.org/.

Permission is granted to use, copy, create derivative works, and redistribute

this software, and any such derivative works, providing that the following

conditions are met:

1.	No fee is charged for all noncommercial education and research purposes;

2.	Redistributions of source code must retain the above copyright notice, this

	list of conditions and the following disclaimer;

3.	Redistributions in binary form must reproduce the above copyright notice,

	this list of conditions and the following disclaimer in the documentation

	and/or other materials provided with the distribution;

4.	Neither the name of the iPlant Collaborative, BIO5, The University of

	Arizona, The University of Texas at Austin, Cold Spring Harbor Laboratory,

	nor the names of other contributors may be used to endorse or promote

	products derived from this software without specific prior written

	permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND

ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR

ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES

(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON

ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.