Apache License
                           Version 2.0, January 2004
                        http://www.apache.org/licenses/

   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

   1. Definitions.

      "License" shall mean the terms and conditions for use, reproduction,
      and distribution as defined by Sections 1 through 9 of this document.

      "Licensor" shall mean the copyright owner or entity authorized by
      the copyright owner that is granting the License.

      "Legal Entity" shall mean the union of the acting entity and all
      other entities that control, are controlled by, or are under common
      control with that entity. For the purposes of this definition,
      "control" means (i) the power, direct or indirect, to cause the
      direction or management of such entity, whether by contract or
      otherwise, or (ii) ownership of fifty percent (50%) or more of the
      outstanding shares, or (iii) beneficial ownership of such entity.

      "You" (or "Your") shall mean an individual or Legal Entity
      exercising permissions granted by this License.

      "Source" form shall mean the preferred form for making modifications,
      including but not limited to software source code, documentation
      source, and configuration files.

      "Object" form shall mean any form resulting from mechanical
      transformation or translation of a Source form, including but
      not limited to compiled object code, generated documentation,
      and conversions to other media types.

      "Work" shall mean the work of authorship, whether in Source or
      Object form, made available under the License, as indicated by a
      copyright notice that is included in or attached to the work
      (an example is provided in the Appendix below).

      "Derivative Works" shall mean any work, whether in Source or Object
      form, that is based on (or derived from) the Work and for which the
      editorial revisions, annotations, elaborations, or other modifications
      represent, as a whole, an original work of authorship. For the purposes
      of this License, Derivative Works shall not include works that remain
      separable from, or merely link (or bind by name) to the interfaces of,
      the Work and Derivative Works thereof.

      "Contribution" shall mean any work of authorship, including
      the original version of the Work and any modifications or additions
      to that Work or Derivative Works thereof, that is intentionally
      submitted to Licensor for inclusion in the Work by the copyright owner
      or by an individual or Legal Entity authorized to submit on behalf of
      the copyright owner. For the purposes of this definition, "submitted"
      means any form of electronic, verbal, or written communication sent
      to the Licensor or its representatives, including but not limited to
      communication on electronic mailing lists, source code control systems,
      and issue tracking systems that are managed by, or on behalf of, the
      Licensor for the purpose of discussing and improving the Work, but
      excluding communication that is conspicuously marked or otherwise
      designated in writing by the copyright owner as "Not a Contribution."

      "Contributor" shall mean Licensor and any individual or Legal Entity
      on behalf of whom a Contribution has been received by Licensor and
      subsequently incorporated within the Work.

   2. Grant of Copyright License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      copyright license to reproduce, prepare Derivative Works of,
      publicly display, publicly perform, sublicense, and distribute the
      Work and such Derivative Works in Source or Object form.

   3. Grant of Patent License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      (except as stated in this section) patent license to make, have made,
      use, offer to sell, sell, import, and otherwise transfer the Work,
      where such license applies only to those patent claims licensable
      by such Contributor that are necessarily infringed by their
      Contribution(s) alone or by combination of their Contribution(s)
      with the Work to which such Contribution(s) was submitted. If You
      institute patent litigation against any entity (including a
      cross-claim or counterclaim in a lawsuit) alleging that the Work
      or a Contribution incorporated within the Work constitutes direct
      or contributory patent infringement, then any patent licenses
      granted to You under this License for that Work shall terminate
      as of the date such litigation is filed.

   4. Redistribution. You may reproduce and distribute copies of the
      Work or Derivative Works thereof in any medium, with or without
      modifications, and in Source or Object form, provided that You
      meet the following conditions:

      (a) You must give any other recipients of the Work or
          Derivative Works a copy of this License; and

      (b) You must cause any modified files to carry prominent notices
          stating that You changed the files; and

      (c) You must retain, in the Source form of any Derivative Works
          that You distribute, all copyright, patent, trademark, and
          attribution notices from the Source form of the Work,
          excluding those notices that do not pertain to any part of
          the Derivative Works; and

      (d) If the Work includes a "NOTICE" text file as part of its
          distribution, then any Derivative Works that You distribute must
          include a readable copy of the attribution notices contained
          within such NOTICE file, excluding those notices that do not
          pertain to any part of the Derivative Works, in at least one
          of the following places: within a NOTICE text file distributed
          as part of the Derivative Works; within the Source form or
          documentation, if provided along with the Derivative Works; or,
          within a display generated by the Derivative Works, if and
          wherever such third-party notices normally appear. The contents
          of the NOTICE file are for informational purposes only and
          do not modify the License. You may add Your own attribution
          notices within Derivative Works that You distribute, alongside
          or as an addendum to the NOTICE text from the Work, provided
          that such additional attribution notices cannot be construed
          as modifying the License.

      You may add Your own copyright statement to Your modifications and
      may provide additional or different license terms and conditions
      for use, reproduction, or distribution of Your modifications, or
      for any such Derivative Works as a whole, provided Your use,
      reproduction, and distribution of the Work otherwise complies with
      the conditions stated in this License.

   5. Submission of Contributions. Unless You explicitly state otherwise,
      any Contribution intentionally submitted for inclusion in the Work
      by You to the Licensor shall be under the terms and conditions of
      this License, without any additional terms or conditions.
      Notwithstanding the above, nothing herein shall supersede or modify
      the terms of any separate license agreement you may have executed
      with Licensor regarding such Contributions.

   6. Trademarks. This License does not grant permission to use the trade
      names, trademarks, service marks, or product names of the Licensor,
      except as required for reasonable and customary use in describing the
      origin of the Work and reproducing the content of the NOTICE file.

   7. Disclaimer of Warranty. Unless required by applicable law or
      agreed to in writing, Licensor provides the Work (and each
      Contributor provides its Contributions) on an "AS IS" BASIS,
      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
      implied, including, without limitation, any warranties or conditions
      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
      PARTICULAR PURPOSE. You are solely responsible for determining the
      appropriateness of using or redistributing the Work and assume any
      risks associated with Your exercise of permissions under this License.

   8. Limitation of Liability. In no event and under no legal theory,
      whether in tort (including negligence), contract, or otherwise,
      unless required by applicable law (such as deliberate and grossly
      negligent acts) or agreed to in writing, shall any Contributor be
      liable to You for damages, including any direct, indirect, special,
      incidental, or consequential damages of any character arising as a
      result of this License or out of the use or inability to use the
      Work (including but not limited to damages for loss of goodwill,
      work stoppage, computer failure or malfunction, or any and all
      other commercial damages or losses), even if such Contributor
      has been advised of the possibility of such damages.

   9. Accepting Warranty or Additional Liability. While redistributing
      the Work or Derivative Works thereof, You may choose to offer,
      and charge a fee for, acceptance of support, warranty, indemnity,
      or other liability obligations and/or rights consistent with this
      License. However, in accepting such obligations, You may act only
      on Your own behalf and on Your sole responsibility, not on behalf
      of any other Contributor, and only if You agree to indemnify,
      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
      of your accepting any such warranty or additional liability.

   END OF TERMS AND CONDITIONS

   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
      boilerplate notice, with the fields enclosed by brackets "{}"
      replaced with your own identifying information. (Don't include
      the brackets!)  The text should be enclosed in the appropriate
      comment syntax for the file format. We also recommend that a
      file or class name and description of purpose be included on the
      same "printed page" as the copyright notice for easier
      identification within third-party archives.

   Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.


ENSEMBL WEBCODE PROJECT SUBCOMPONENTS

The Ensembl Webcode Project includes a number of subcomponents with
separate copyright notices and license terms. Your use of the source
code for the these subcomponents is subject to the terms and
conditions of the following licenses.

COMPONENT: modules/Pack.pm
           modules/ParseMaster.pm

Based on Pack.js and ParseMaster.js by Dean Edwards http://dean.edwards.name/
Ported to Perl by Rob Seiler, ELR Software Pty Ltd http://www.elr.com.au
Copyright 2005. License http://creativecommons.org/licenses/LGPL/2.1/

COMPONENT: utils/static_content/doxygen/bin/doxygenfilter
           htdocs/info/docs/Doxygen/doxygen.css

Both portions of code were based on the following agreement; 
doxygen.css was made by merging multiple css files provided by Doxygen into one, 
then adding some Ensembl-specific requirements.

Doxygen Pre-Processor for Perl
Copyright (C) 2002  Bart Schuller
Copyright (C) 2006  Phinex Informatik AG
All Rights Reserved

Doxygen Filter is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

Larry Wall's 'Artistic License' for perl can be found in
http://www.perl.com/pub/a/language/misc/Artistic.html

COMPONENT: modules/CSS/Minifier.pm
           modules/JavaScript/Minifier.pm

Copyright (C) 2007 by Peter Michaux

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.6 or,
at your option, any later version of Perl 5 you may have available.

COMPONENT: modules/Bio/Das/Lite.pm

Copyright (C) 2007 GRL, by Roger Pettett

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.4 or,
at your option, any later version of Perl 5 you may have available.

COMPONENT: htdocs/components/00_Base.js
           htdocs/components/00_jquery.js
           htdocs/components/00_jquery_ui.js
           htdocs/components/00_jquery_hoverintent.js
           htdocs/raphael/
           
These libraries are all provided under the MIT license http://opensource.org/licenses/MIT
           
Base.js            Copyright 2006-2007, Dean Edwards
jQuery             Copyright 2005, 2012 jQuery Foundation, Inc.
jQuery UI          Copyright 2013 jQuery Foundation and other contributors
jQuery hoverIntent Copyright 2007, 2013 Brian Cherne
Rapha?l JS         Copyright 2010 Dmitry Baranovskiy

COMPONENT: htdocs/components/00_jquery_hashchange.js

This code has been modified slightly to work with jQuery 1.9 

Copyright (c) 2010 "Cowboy" Ben Alman
Dual licensed under the MIT and GPL licenses.
http://benalman.com/about/license/

COMPONENT: htdocs/components/00_jquery_dataTables.js

Copyright 2008-2012 Allan Jardine, all rights reserved.

This source file is free software, under either the GPL v2 license or a
BSD style license, available at:
  http://datatables.net/license_gpl2
  http://datatables.net/license_bsd

This source file 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 license files for details.

COMPONENT: htdocs/info/docs/api/compara/highlight.css

Generated by highlight 3.9, http://www.andre-simon.de/

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

COMPONENT: htdocs/jalview/

The Jalview source is made available under the GNU General Public License (v3) as a gzipped tar file, which expands to a directory named jalview.

COMPONENT: utils/compression/compiler.jar

The Google Closure Compiler is distributed under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)

COMPONENT: utils/compression/yuicompressor-2.4.7.jar

All code specific to YUI Compressor is issued under a BSD license (http://yui.github.io/yui/license.html). 
YUI Compressor extends and implements code from Mozilla's Rhino project (http://www.mozilla.org/rhino/). 
Rhino is issued under the Mozilla Public License (MPL) (http://www.mozilla.org/MPL/), and MPL applies to the Rhino source and binaries that are distributed with YUI Compressor, 
including Rhino modifications made by YUI Compressor. 
YUI Compressor also makes use of and distributes a binary of JArgs (http://jargs.sourceforge.net/); the JArgs BSD license applies to this binary.

COMPONENT: utils/spider/spider.pl

Copyright (C) 2001-2003 Bill Moseley [email protected]

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.

COMPONENT: utils/edoc/support/scriptaculous.js
           utils/edoc/support/controls.js
           utils/edoc/support/dragdrop.js
           utils/edoc/support/slider.js
           utils/edoc/support/unittest.js

These libraries are all under the same license, with different copyrights, listed below:

utils/edoc/support/controls.js
Copyright (c) 2005 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
          (c) 2005 Ivan Krstic (http://blogs.law.harvard.edu/ivan)
          (c) 2005 Jon Tirsen (http://www.tirsen.com)
          
          
utils/edoc/support/dragdrop.js
Copyright (c) 2005 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
          (c) 2005 Sammi Williams (http://www.oriontransfer.co.nz, [email protected])

utils/edoc/support/slider.js
Copyright (c) 2005 Marty Haught, Thomas Fuchs           
           
utils/edoc/support/unittest.js
(c) 2005 Jon Tirsen (http://www.tirsen.com)
(c) 2005 Michael Schuerig (http://www.schuerig.de/michael/)

Copyright (c) 2005 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

COMPONENT: utils/edoc/support/prototype.js

(c) 2005 Sam Stephenson <[email protected]>

Prototype is freely distributable under the terms of an MIT-style license.
For details, see the Prototype web site: http://prototype.conio.net/