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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
author lecorguille
date Tue, 01 Nov 2016 17:12:07 -0400
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31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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1 Galaxy wrapper for HMMER3
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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2 =========================
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4 This wrapper is copyright 2015 by Eric Rasche
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6 HMMER is used for searching sequence databases for homologs of protein
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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7 sequences, and for making protein sequence alignments. It implements methods
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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8 using probabilistic models called profile hidden Markov models (profile HMMs).
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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10 Compared to BLAST, FASTA, and other sequence alignment and database search
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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11 tools based on older scoring methodology, HMMER aims to be significantly more
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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12 accurate and more able to detect remote homologs because of the strength of its
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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13 underlying mathematical models. In the past, this strength came at significant
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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14 computational expense, but in the new HMMER3 project, HMMER is now essentially
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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15 as fast as BLAST.
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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17 http://hmmer.janelia.org/
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18 http://hmmer.janelia.org/about
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21 Installation
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22 ============
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24 The recommended installation is by means of the toolshed_.
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3
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29 History
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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30 =======
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32 * v0.2 - Add build-in hmm database for hmmscan and hmmsearch
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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33 * v0.1 - Initial public release
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36 Licence (MIT)
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37 =============
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39 Permission is hereby granted, free of charge, to any person obtaining a copy
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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40 of this software and associated documentation files (the "Software"), to deal
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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41 in the Software without restriction, including without limitation the rights
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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42 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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43 copies of the Software, and to permit persons to whom the Software is
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44 furnished to do so, subject to the following conditions:
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46 The above copyright notice and this permission notice shall be included in
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47 all copies or substantial portions of the Software.
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49 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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50 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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51 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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52 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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53 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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54 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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55 THE SOFTWARE.