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NOTICE
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Please report bugs to:
Alexie Papanicolaou
Hawkesbury Institute for the Environment, Western Sydney University, Richmond NSW, Australia
=============================================================================================================
LEGALESE
LICENSE
This software is released under the terms specified in LICENSE file. This Open-Source LICENSE gives you
certain rights under certain terms for using the software, please respect them.
This software contains or links code from the following software each of which may fall under a particular notice:
== The following tools contributed code which may have been modified.
PASA (PerlLib)
==============
http://pasa.sourceforge.net/
Copyright (c) 2012, The Broad Institute, Inc. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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.
Neither the name of the Broad Institute 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 BROAD INSTITUTE ''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 BROAD INSTITUTE
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.
== The following tools are linked/aggregated without modifications:
Perl modules
============
Are linked and licensed under the Artistic License v1 or v2 depending on your Perl version
http://www.perl.org
cdbtools
========
Artistic License
http://compbio.dfci.harvard.edu/tgi/software/
http://compbio.dfci.harvard.edu/tgi/software/artistic.html
The Gene Index Project and tools is supported in part by funding from the US Department of Energy, Grant #DE-FG02-99ER62852,
and the US National Science Foundation, Grant #DBI-9983070. Additional funds are provided by the US National Science Foundation through grants #DBI-9813392 and #DBI-9975866.
parafly, transdecoder and aatpackage, justpreprocessmyreads, PASA, evidencemodeler
==============================================================================
See open licenses. We're also the (co-)authors of these software:
See 3rd_party/parafly/LICENSE
See 3rd_party/transdecoder/LICENSE
http://sourceforge.net/projects/parafly
http://sourceforge.net/projects/transdecoder
PHP code/functions
==================
BSD license
http://www.php.net/license
d3
==
BSD license
Wordcloud d3
============
MIT license
CanvasXpress
============
http://canvasxpress.org
Commercial License to CSIRO (otherwise GPL for all other users)
ExtJS
=====
http://extjs.com
Commercial License
http://www.sencha.com/legal/sencha-sdk-software-license-agreement
hhsuite/hhblits
===============
Is distributed under the GPL license. Copyleft does not apply due to the aggregation terms:
ftp://toolkit.genzentrum.lmu.de/pub/HHblits/