We borrowed some code from samtools (http://www.htslib.org/), which
is MIT-licensed:

    The MIT/Expat License

    Copyright (C) 2008-2014 Genome Research Ltd.

    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.

In the web visualizer, we use D3 (https://d3js.org/), which is
BSD-licensed:

    Copyright 2010-2016 Mike Bostock
    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 author nor the names of 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 OWNER 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.

And DataTables (https://datatables.net/), MIT-licensed:

    Copyright (C) 2008-2016, SpryMedia Ltd.

    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.

For the DataTables Excel export, JSZip (https://github.com/Stuk/jszip)
is used; it's available under the MIT (included here) or GPLv3 license:

    Copyright (c) 2009-2016 Stuart Knightley, David Duponchel, Franz
    Buchinger, António Afonso

    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.

Also, normalize.css (https://github.com/necolas/normalize.css),
MIT-licensed:

    Copyright © Nicolas Gallagher and Jonathan Neal

    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.

And SpinKit (https://github.com/tobiasahlin/SpinKit), MIT-licensed:

    The MIT License (MIT)

    Copyright (c) 2015 Tobias Ahlin

    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.

The fonts used in the web visualizer are licensed under the SIL Open
Font License:

    -----------------------------------------------------------
    SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
    -----------------------------------------------------------

    PREAMBLE

    The goals of the Open Font License (OFL) are to stimulate
    worldwide development of collaborative font projects, to support
    the font creation efforts of academic and linguistic communities,
    and to provide a free and open framework in which fonts may be
    shared and improved in partnership with others.

    The OFL allows the licensed fonts to be used, studied, modified
    and redistributed freely as long as they are not sold by
    themselves. The fonts, including any derivative works, can be
    bundled, embedded, redistributed and/or sold with any software
    provided that any reserved names are not used by derivative
    works. The fonts and derivatives, however, cannot be released
    under any other type of license. The requirement for fonts to
    remain under this license does not apply to any document created
    using the fonts or their derivatives.

    DEFINITIONS

    "Font Software" refers to the set of files released by the
    Copyright Holder(s) under this license and clearly marked as
    such. This may include source files, build scripts and
    documentation.

    "Reserved Font Name" refers to any names specified as such after
    the copyright statement(s).

    "Original Version" refers to the collection of Font Software
    components as distributed by the Copyright Holder(s).

    "Modified Version" refers to any derivative made by adding to,
    deleting, or substituting -- in part or in whole -- any of the
    components of the Original Version, by changing formats or by
    porting the Font Software to a new environment.

    "Author" refers to any designer, engineer, programmer, technical
    writer or other person who contributed to the Font Software.

    PERMISSION & CONDITIONS

    Permission is hereby granted, free of charge, to any person
    obtaining a copy of the Font Software, to use, study, copy, merge,
    embed, modify, redistribute, and sell modified and unmodified
    copies of the Font Software, subject to the following conditions:

    1) Neither the Font Software nor any of its individual components,
    in Original or Modified Versions, may be sold by itself.

    2) Original or Modified Versions of the Font Software may be
    bundled, redistributed and/or sold with any software, provided
    that each copy contains the above copyright notice and this
    license. These can be included either as stand-alone text files,
    human-readable headers or in the appropriate machine-readable
    metadata fields within text or binary files as long as those
    fields can be easily viewed by the user.

    3) No Modified Version of the Font Software may use the Reserved
    Font Name(s) unless explicit written permission is granted by the
    corresponding Copyright Holder. This restriction only applies to
    the primary font name as presented to the users.

    4) The name(s) of the Copyright Holder(s) or the Author(s) of the
    Font Software shall not be used to promote, endorse or advertise
    any Modified Version, except to acknowledge the contribution(s) of
    the Copyright Holder(s) and the Author(s) or with their explicit
    written permission.

    5) The Font Software, modified or unmodified, in part or in whole,
    must be distributed entirely under this license, and must not be
    distributed under any other license. The requirement for fonts to
    remain under this license does not apply to any document created
    using the Font Software.

    TERMINATION

    This license becomes null and void if any of the above conditions
    are not met.

    DISCLAIMER

    THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
    KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY
    WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE
    AND NONINFRINGEMENT OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER
    RIGHT. IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE FOR ANY
    CLAIM, DAMAGES OR OTHER LIABILITY, INCLUDING ANY GENERAL, SPECIAL,
    INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, WHETHER IN AN
    ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF THE
    USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER DEALINGS
    IN THE FONT SOFTWARE.

Source Sans Pro is Copyright 2010, 2012, 2014 Adobe Systems
Incorporated (http://www.adobe.com/), with Reserved Font Name
'Source'. All Rights Reserved. Source is a trademark of Adobe Systems
Incorporated in the United States and/or other countries.

Font Awesome was made by Dave Gandy, for which we thank him. It truly
is awesome.

The export of the web viewer plots uses code from
https://stackoverflow.com/a/44769098, which according to the Stack
Overflow terms of service is licensed under CC BY-SA 3.0
(https://creativecommons.org/licenses/by-sa/3.0/).
