Mercurial > repos > iuc > hmmer_alimask

annotate readme.rst @ 0:a20b2c7c5eee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
author iuc
date Sat, 25 Jun 2016 15:04:25 -0400
parents
children 70cdf5a19b4b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
1 Galaxy wrapper for HMMER3
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
2 =========================
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
3
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
4 This wrapper is copyright 2015 by Eric Rasche
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
5
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
6 HMMER is used for searching sequence databases for homologs of protein
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
7 sequences, and for making protein sequence alignments. It implements methods
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
8 using probabilistic models called profile hidden Markov models (profile HMMs).
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
9
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
10 Compared to BLAST, FASTA, and other sequence alignment and database search
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
11 tools based on older scoring methodology, HMMER aims to be significantly more
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
12 accurate and more able to detect remote homologs because of the strength of its
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
13 underlying mathematical models. In the past, this strength came at significant
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
14 computational expense, but in the new HMMER3 project, HMMER is now essentially
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
15 as fast as BLAST.
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
16
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
17 http://hmmer.janelia.org/
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
18 http://hmmer.janelia.org/about
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
19
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
20
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
21 Installation
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
22 ============
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
23
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
24 The recommended installation is by means of the toolshed_.
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
25
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
27
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
28
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
29 History
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
30 =======
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
31
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
32 * v0.1 - Initial public release
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
33
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
34
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
35 Licence (MIT)
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
36 =============
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
37
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
38 Permission is hereby granted, free of charge, to any person obtaining a copy
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
39 of this software and associated documentation files (the "Software"), to deal
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
40 in the Software without restriction, including without limitation the rights
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
41 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
42 copies of the Software, and to permit persons to whom the Software is
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
43 furnished to do so, subject to the following conditions:
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
44
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
45 The above copyright notice and this permission notice shall be included in
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
46 all copies or substantial portions of the Software.
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
47
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
48 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
49 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
50 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
51 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
52 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
53 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
54 THE SOFTWARE.