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Galaxy wrapper for HMMER3
=========================

This wrapper is copyright 2015 by Eric Rasche

HMMER is used for searching sequence databases for homologs of protein
sequences, and for making protein sequence alignments. It implements methods
using probabilistic models called profile hidden Markov models (profile HMMs).

Compared to BLAST, FASTA, and other sequence alignment and database search
tools based on older scoring methodology, HMMER aims to be significantly more
accurate and more able to detect remote homologs because of the strength of its
underlying mathematical models. In the past, this strength came at significant
computational expense, but in the new HMMER3 project, HMMER is now essentially
as fast as BLAST.

http://hmmer.janelia.org/
http://hmmer.janelia.org/about


Installation
============

The recommended installation is by means of the toolshed_.

.. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3


History
=======

* v0.1.1    - hmmscan: add the possibility to scan a built-in hmm profile database
* v0.1      - Initial public release


Licence (MIT)
=============

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.