Mercurial > repos > iuc > package_hmmer_3_1b1

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 18d253be0ca437eb06477753fb7a962124cb0428
author iuc
date Mon, 25 Jan 2016 14:52:42 -0500
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e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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1 <?xml version="1.0"?>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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2 <tool_dependency>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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3 <package name="hmmer" version="3.1b1">
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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4 <install version="1.0">
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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5 <actions>
1
ee143f73fee0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 18d253be0ca437eb06477753fb7a962124cb0428
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6 <action type="download_by_url" sha256sum="246f5e32545d3a5706d065d8413fc8fc5445e779a97019e98ba319e5ef9dc1d8">
ee143f73fee0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 18d253be0ca437eb06477753fb7a962124cb0428
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7 https://depot.galaxyproject.org/software/hmmer/hmmer_3.1b1_src_all.tar.gz
ee143f73fee0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 18d253be0ca437eb06477753fb7a962124cb0428
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8 </action>
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e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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9 <action type="autoconf" />
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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10 <action type="change_directory">easel/miniapps/</action>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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11 <action type="make_install" />
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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12 <action type="set_environment">
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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13 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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14 <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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15 <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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17 </action>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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18 </actions>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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19 </install>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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20 <readme>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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21 HMMER is used for searching sequence databases for homologs of protein
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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22 sequences, and for making protein sequence alignments. It implements methods
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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23 using probabilistic models called profile hidden Markov models (profile HMMs).
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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24
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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25 Compared to BLAST, FASTA, and other sequence alignment and database search
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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26 tools based on older scoring methodology, HMMER aims to be significantly more
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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27 accurate and more able to detect remote homologs because of the strength of its
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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28 underlying mathematical models. In the past, this strength came at significant
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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29 computational expense, but in the new HMMER3 project, HMMER is now essentially
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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30 as fast as BLAST.
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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31
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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32 As part of this evolution in the HMMER software, we are committed to making the
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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33 software available to as many scientists as possible. Earlier releases of HMMER
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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34 were restricted to command line use. To make the software more accessible to
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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35 the wide scientific community, we now provide servers that allow sequence
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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36 searches to be performed interactively via the Web.
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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37
1
ee143f73fee0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 18d253be0ca437eb06477753fb7a962124cb0428
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38 http://hmmer.org/
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e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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39 </readme>
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40 </package>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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41 </tool_dependency>