Mercurial > repos > iuc > hmmer_hmmbuild

annotate readme.rst @ 10:51970d0e7bd7 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 e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:40:07 +0000
parents 9c09de38e2b2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
1 Galaxy wrapper for HMMER3
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
2 =========================
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
3
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
4 This wrapper is copyright 2015 by Eric Rasche
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
5
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
6 HMMER is used for searching sequence databases for homologs of protein
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
7 sequences, and for making protein sequence alignments. It implements methods
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
8 using probabilistic models called profile hidden Markov models (profile HMMs).
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
9
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
10 Compared to BLAST, FASTA, and other sequence alignment and database search
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
11 tools based on older scoring methodology, HMMER aims to be significantly more
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
12 accurate and more able to detect remote homologs because of the strength of its
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
13 underlying mathematical models. In the past, this strength came at significant
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
14 computational expense, but in the new HMMER3 project, HMMER is now essentially
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
15 as fast as BLAST.
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
16
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
17 http://hmmer.janelia.org/
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
18 http://hmmer.janelia.org/about
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
19
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
20
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
21 Installation
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
22 ============
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
23
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
24 The recommended installation is by means of the toolshed_.
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
25
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
27
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
28
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
29 History
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
30 =======
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
31
3
9c09de38e2b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents: 0
diff changeset
32 * v0.1.1 - hmmscan: add the possibility to scan a built-in hmm profile database
0
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
33 * v0.1 - Initial public release
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
34
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
35
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
36 Licence (MIT)
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
37 =============
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
38
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
39 Permission is hereby granted, free of charge, to any person obtaining a copy
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
40 of this software and associated documentation files (the "Software"), to deal
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
41 in the Software without restriction, including without limitation the rights
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
42 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
43 copies of the Software, and to permit persons to whom the Software is
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
44 furnished to do so, subject to the following conditions:
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
45
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
46 The above copyright notice and this permission notice shall be included in
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
47 all copies or substantial portions of the Software.
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
48
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
49 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
50 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
51 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
52 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
53 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
54 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
648d9e133324 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
55 THE SOFTWARE.