forked from genomecuration/JAMg
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NOTICE
163 lines (128 loc) · 6.56 KB
/
NOTICE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
Please report bugs to:
Alexie Papanicolaou
1 CSIRO Ecosystem Sciences, GPO 1700, Canberra 2601, 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 unless mentioned:
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.
snap
====
Is distributed under the MIT license.
http://korflab.ucdavis.edu/software.html
glimmerhmm
==========
Copyright (c) 2005 by Mihaela Pertea. Artistic License
http://ccb.jhu.edu/software/glimmerhmm/
augustus
========
Is distributed under the Artistic license
http://augustus.gobics.de/
gmap
====
See 3rd_party/gmap/COPYING and 3rd_party/gmap/NOTICE
http://research-pub.gene.com/gmap/
RepeatMasker
============
See http://www.repeatmasker.org, distributed under license (3rd_party/RepeatMasker/license.txt).
Also included already are the RMBLAST and BLAST+ executables from NCBI (which are in the Public Domain, see License in 3rd_party/RepeatMasker/ncbi-blast)
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST/ncbi-rmblastn-2.2.28-x64-linux.tar.gz
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.28+-x64-linux.tar.gz
geneid
======
http://genome.crg.es/software/geneid
Distributed under GPL's aggregation terms:
A compilation of a covered work with other separate and independent
works, which are not by their nature extensions of the covered work,
and which are not combined with it such as to form a larger program,
in or on a volume of a storage or distribution medium, is called an
"aggregate" if the compilation and its resulting copyright are not
used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate. [http://www.gnu.org/licenses/gpl.html]
blat
====
See http://users.soe.ucsc.edu/~kent/src
Distributed under GPL's aggregation terms:
exonerate
=========
See http://www.ebi.ac.uk/~guy/exonerate
Distributed under GPL's aggregation terms:
Samtools
========
Distributed under GPL's aggregation terms
http://samtools.sourceforge.net/
We modified the Makefile to not install the LIBCURSES GUI
Bedtools
========
Distributed under GPL's aggregation terms
http://code.google.com/p/bedtools
hhsuite/hhblits
===============
Distributed under GPL's aggregation terms
ftp://toolkit.genzentrum.lmu.de/pub/HHblits/
parafly, transdecoder and aatpackage, justpreprocessmyreads, PASA, evidencemodeler
==============================================================================
See open licenses. We're also the (co-)authors of these software:
See 3rd_party/PASA/LICENSE
See 3rd_party/parafly/LICENSE
See 3rd_party/aatpackage/LICENSE
See 3rd_party/transdecoder/LICENSE
See 3rd_party/evidencemodeler/LICENSE
See 3rd_party/justpreprocessmyreads/LICENSE
http://sourceforge.net/projects/pasa
http://sourceforge.net/projects/parafly
http://sourceforge.net/projects/aatpackage
http://sourceforge.net/projects/transdecoder
http://sourceforge.net/projects/evidencemodeler
http://justpreprocessmyreads.sourceforge.net/
eval
====
Written, copywrite and maintained by Robert Paul Zimmermann <[email protected]>
Distributed under the agglomeration terms of GPL (see eval-2.2.8/debian/copyright)
The PHP/Java Bridge PHP library (WebApollo/ws/Java)
===================================================
Compiled from JavaBridge.inc.
Copyright (C) 2003-2009 Jost Boekemeier.
Distributed under the MIT license, see Options.inc for details.
CEGMA
=====
CEGMA has been written by Genis Parra (formerly at UC Davis Genome Center) and subsequently updated
by Keith Bradnam ([email protected]). CEGMA home page is at "http://korflab.ucdavis.edu/Datasets/cegma/"
Distributed under GPL's aggregation terms
Mauve
=====
Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary
events such as rearrangement and inversion. See http://gel.ahabs.wisc.edu/mauve/mauve-user-guide
Contact darling(at)cs.wisc.edu
Mauve is licensed under the GNU GPL and distributed under GPL's aggregation terms