Mercurial > repos > lecorguille > hmmer_alimask

annotate readme.rst @ 0:4b708697e529 draft default tip

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 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
author lecorguille
date Tue, 01 Nov 2016 17:11:23 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
1 Galaxy wrapper for HMMER3
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
2 =========================
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
3
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
4 This wrapper is copyright 2015 by Eric Rasche
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
5
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
6 HMMER is used for searching sequence databases for homologs of protein
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
7 sequences, and for making protein sequence alignments. It implements methods
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
8 using probabilistic models called profile hidden Markov models (profile HMMs).
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
9
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
10 Compared to BLAST, FASTA, and other sequence alignment and database search
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
11 tools based on older scoring methodology, HMMER aims to be significantly more
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
12 accurate and more able to detect remote homologs because of the strength of its
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
13 underlying mathematical models. In the past, this strength came at significant
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
14 computational expense, but in the new HMMER3 project, HMMER is now essentially
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
15 as fast as BLAST.
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
16
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
17 http://hmmer.janelia.org/
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
18 http://hmmer.janelia.org/about
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
19
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
20
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
21 Installation
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
22 ============
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
23
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
24 The recommended installation is by means of the toolshed_.
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
25
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
27
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
28
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
29 History
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
30 =======
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
31
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
32 * v0.2 - Add build-in hmm database for hmmscan and hmmsearch
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
33 * v0.1 - Initial public release
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
34
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
35
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
36 Licence (MIT)
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
37 =============
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
38
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
39 Permission is hereby granted, free of charge, to any person obtaining a copy
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
40 of this software and associated documentation files (the "Software"), to deal
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
41 in the Software without restriction, including without limitation the rights
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
42 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
43 copies of the Software, and to permit persons to whom the Software is
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
44 furnished to do so, subject to the following conditions:
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
45
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
46 The above copyright notice and this permission notice shall be included in
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
47 all copies or substantial portions of the Software.
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
48
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
49 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
50 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
51 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
52 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
53 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
54 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
4b708697e529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
parents:
diff changeset
55 THE SOFTWARE.