Copyright Notice#

PyHMMER#

The PyHMMER library is developed under the MIT license:

Copyright (c) 2020-2024 Martin Larralde <martin.larralde@embl.de>

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.

PyHMMER development was supported by the European Molecular Biology Laboratory; the SFB 1371 of the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) [grant number 395357507] and the Federal Ministry of Education and Research (BMBF) [grant number 031L0181A].

Easel#

PyHMMER distributes, builds and links to code from the Easel library, redistributed under the terms of the BSD license:

Copyright (C) 1990-2023 Sean R. Eddy
Copyright (C) 2015-2023 President and Fellows of Harvard College
Copyright (C) 2000-2023 Howard Hughes Medical Institute
Copyright (C) 1995-2006 Washington University School of Medicine
Copyright (C) 1992-1995 MRC Laboratory of Molecular Biology, UK

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.

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.

Easel’s code includes contributions from members of the Eddy/Rivas laboratory at Harvard University, the HMMER and Infernal development teams, and other colleagues, including:

Tyler Camp
Nick Carter
Michael Farrar
Graeme Mitchison
Eric Nawrocki
Sam Petti
Elena Rivas
Travis Wheeler

Easel also includes code we have incorporated from other sources and authors – including public domain code, and licensed copyrighted code. Sources and licenses are noted in the appropriate places in individual files. Copyright holders and contributors include:

Barry W. Brown, James Lovato: esl_random:esl_rnd_Gaussian()
Bob Jenkins: esl_random::esl_rnd_mix3()
Steven G. Johnson, and others: autoconf macros in m4/
Martin Larralde: ARM Neon support
Kevin Lawler: esl_rand64::esl_rand64_Deal()
Stephen Moshier: SIMD vectorized logf, expf
Takuji Nishimura, Makoto Matsumoto: esl_random, esl_rand64
Julien Pommier: SIMD vectorized logf,``expf``
David Robert Nadeau: esl_stopwatch
Henry Spencer: esl_regexp
David Wheeler: easel::esl_tmpfile()
Free Software Foundation, Inc.: configure
FreeBSD: easel::esl_strsep()
Sun Microsystems, Inc.: esl_stats::esl_erfc()

Easel development is supported in part by the National Human Genome Research Institute of the US National Institutes of Health under grant number R01HG009116. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

HMMER#

PyHMMER distributes, builds and links to code from the HMMER software, redistributed under the terms of the BSD-3-clause license:

Copyright (C) 1992-2023 Sean R. Eddy
Copyright (C) 2015-2023 President and Fellows of Harvard College
Copyright (C) 2000-2023 Howard Hughes Medical Institute
Copyright (C) 1995-2006 Washington University School of Medicine
Copyright (C) 1992-1995 MRC Laboratory of Molecular Biology

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 any copyright holder 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 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.

The code includes contributions and input from current and past members of the HMMER development team, as well as other colleagues and sources, including:

Bill Arndt
Jeremy Buhler
Tyler Camp
Nick Carter
Sergi Castellano
Goran Ceric
Michael Farrar
Rob Finn
Ian Holmes
Bjarne Knudsen
Diana Kolbe
Martin Larralde
Erik Lindahl
Graeme Mitchison
Eric Nawrocki
Lee Newberg
Sam Petti
Elena Rivas
Walt Shands
Travis Wheeler

HMMER also includes copyrighted and licensed code that has been incorporated from other sources, including:

Yuta Mori (libdivsufsort-lite)
Apple Computer
Free Software Foundation, Inc.
IBM TJ Watson Research Center
X Consortium

HMMER uses the Easel software library, which has its own license and copyright information. See Easel section above.

HMMER includes patent-pending SIMD technology under a nonexclusive license from the estate of Michael Farrar. You are sublicensed to use this technology specifically for the use, modification, and redistribution of HMMER.

HMMER development is supported in part by the National Human Genome Research Institute of the US National Institutes of Health under grant number R01HG009116. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.