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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
author iuc
date Sat, 25 Jun 2016 15:07:00 -0400
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1 Galaxy wrapper for HMMER3
2 =========================
3
4 This wrapper is copyright 2015 by Eric Rasche
5
6 HMMER is used for searching sequence databases for homologs of protein
7 sequences, and for making protein sequence alignments. It implements methods
8 using probabilistic models called profile hidden Markov models (profile HMMs).
9
10 Compared to BLAST, FASTA, and other sequence alignment and database search
11 tools based on older scoring methodology, HMMER aims to be significantly more
12 accurate and more able to detect remote homologs because of the strength of its
13 underlying mathematical models. In the past, this strength came at significant
14 computational expense, but in the new HMMER3 project, HMMER is now essentially
15 as fast as BLAST.
16
17 http://hmmer.janelia.org/
18 http://hmmer.janelia.org/about
19
20
21 Installation
22 ============
23
24 The recommended installation is by means of the toolshed_.
25
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3
27
28
29 History
30 =======
31
32 * v0.1 - Initial public release
33
34
35 Licence (MIT)
36 =============
37
38 Permission is hereby granted, free of charge, to any person obtaining a copy
39 of this software and associated documentation files (the "Software"), to deal
40 in the Software without restriction, including without limitation the rights
41 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
42 copies of the Software, and to permit persons to whom the Software is
43 furnished to do so, subject to the following conditions:
44
45 The above copyright notice and this permission notice shall be included in
46 all copies or substantial portions of the Software.
47
48 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
49 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
50 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
51 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
52 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
53 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
54 THE SOFTWARE.