# Third-party notices and data provenance
This independent Rust implementation is distributed under GPL-3.0-or-later.
The project license is in LICENSE. Upstream code/data retain their applicable
licenses and notices below. Upstream authors do not endorse this implementation.
## CRISPRCasFinder and CasFinder data
Source: https://github.com/dcouvin/CRISPRCasFinder
Reference revision: 9a7f07edc4001875be05f6f0f0eb81f4fdf52e4d
License: GPL-3.0-or-later; upstream COPYING contains the GPL v3 text in LICENSE.
The bundled CasFinder-2.0.3 XML definitions and HMM profiles were compared with
this revision: 152 of 153 files are byte-identical. CAS-TypeIIID.xml removes a
stray `/>` following the Csm2_1_IIIA gene element and one trailing blank line.
The Repeat_List.csv and repeatDirection.tsv files are byte-identical to the
same revision's supplementary_files. The browser model bundle is generated
from these local definitions/profiles. Preserve these notes when changing data.
Upstream copyright notice follows:
```text
CRISPRCasFinder allows to find CRISPR arrays as well as associated cas genes.
Copyright (C) 2017- CRISPR-Cas++ team (CNRS, Université Paris-Saclay, Institut Pasteur, Université de Lille).
------------------------------------------------------------------
Citation:
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C.
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.
Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251. DOI: https://doi.org/10.1093/nar/gky425
------------------------------------------------------------------
All the contributors of the program are:
David Couvin,
Aude Bernheim,
Claire Toffano-Nioche,
Marie Touchon,
Bertrand Néron,
Christine Drevet,
Luis M. Rodriguez,
Lee S. Katz,
Juraj Michalik,
Fabrice Leclerc,
Cyrille Petat,
Arnaud Martel,
Nicolas Villeriot.
-----------------------------------------------------------------
The source code of CRISPRCasFinder is distributed
under the terms of the GNU GeneralPublic License.
See the file COPYING for details.
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 3 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, see .
```
## Vmatch portions
The module crispr-cas-finder-core/src/vmatch.rs is a Rust port of the parts of
Vmatch that CRISPRCasFinder's repeat search goes through: the extension of
exact seeds by greedy unit edit distance alignment (kurtz/extendED.c,
kurtz/frontSEP.c, kurtz/front.gen), the E-values of repeats (kurtz/evalues.c),
the seed length (Vmatch/matchlenparm.c), the acceptance of a repeat
(Vmatch/mokay.c, Vmatch/procfinal.c, Vmatch/SELECT/sel392.c) and the removal of
contained repeats (kurtz/smcontain.c). The enumeration of
maximal exact repeats is written anew and does not use Vmatch's index.
Source: https://github.com/genometools/vstree
Reference revision: 533c8bb9a5dc981bd3f4d1c44adbfcdd68336b89 (Vmatch 2.3.1)
License: ISC.
```text
Copyright (c) 2000-2006 Stefan Kurtz
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
```
The alignment that tells a tandem repeat from an array
(crispr-cas-finder-core/src/conservation.rs, `align_shifted_copies`) uses the
substitution scores and gap penalties MUSCLE 3.8 applies to nucleotides, which
are the BLASTZ defaults. No MUSCLE or EMBOSS code is included.
## HMMER and Easel portions
The internal modules src/hmmer_core and src/hmmer_io include Rust ports of
HMMER and Easel functionality, adapted and modified in this project. They are
not an official HMMER release. The historical port did not record a precise
upstream revision; the following revisions identify the preserved upstream
notice texts and reference implementation, not a claim of an exact source fork.
HMMER reference: 3.4, revision 9acd8b6758a0ca5d21db6d167e0277484341929b
https://github.com/EddyRivasLab/hmmer/blob/9acd8b6758a0ca5d21db6d167e0277484341929b/LICENSE
```text
HMMER - Biological sequence analysis with profile hidden Markov models
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
-----------------------------------------------------------------------
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/LICENSE.
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.
HMMER source code is distributed as open source under the terms of the
BSD three-clause license:
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.
```
Easel notice revision: 07ca83ba9ef0414dba9ce0a9331d465b5eb58f2b
https://github.com/EddyRivasLab/easel/blob/07ca83ba9ef0414dba9ce0a9331d465b5eb58f2b/LICENSE
```text
Easel - a library of C functions for biological sequence analysis
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
-------------------------------------------------------------------
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.
The Easel library is open source software. It is freely distributed
under the terms of the BSD (Berkeley Software Distribution) open
source license:
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.
```
## Orphos and other dependencies
Gene prediction uses orphos-core 0.4.0, distributed under GPL-3.0-or-later:
https://github.com/FullHuman/orphos. Other Rust dependency versions and sources
are recorded in the accompanying Cargo.lock files and retain their own licenses.
These notices document the bundled scientific code and datasets; they do not
relicense third-party dependencies or assert authorship of upstream material.