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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="hmmer" version="3.0">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz</action>
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7 <action type="shell_command">./configure --prefix $INSTALL_DIR</action>
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8 <action type="shell_command">make</action>
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9 <action type="shell_command">make install</action>
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10 <action type="set_environment">
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11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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12 </action>
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13 </actions>
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14 </install>
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15 <readme>
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16 HMMER is used to search sequence databases for homologs of protein sequences, and to make protein
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17 sequence alignments. HMMER can be used to search sequence databases with single query sequences
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18 but it becomes particularly powerful when the query is an multiple sequence alignment of a sequence family.
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19 HMMER makes a profile of the query that assigns a position-specific scoring system for substitutions,
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20 insertions, and deletions. HMMER profiles are probabilistic models called "profile hidden Markov models"
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21 (profile HMMs) (Krogh et al., 1994; Eddy, 1998; Durbin et al., 1998).
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22
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23 Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older
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24 scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote
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25 homologs, because of the strength of its underlying probability models. In the past, this strength came
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26 at a significant computational cost, with profile HMM implementations running about 100x slower than
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27 comparable BLAST searches. With HMMER3, HMMER is now essentially as fast as BLAST.
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28
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29 The programs in HMMER::
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30
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31 Single sequence queries: new to HMMER3::
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32
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33 phmmer Search a sequence against a sequence database. (BLASTP-like)
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34 jackhmmer Iteratively search a sequence against a sequence database. (PSIBLAST-like)
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35
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36 Replacements for HMMER2's functionality::
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37
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38 hmmbuild Build a pro#le HMM from an input multiple alignment.
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39 hmmsearch Search a pro#le HMM against a sequence database.
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40 hmmscan Search a sequence against a pro#le HMM database.
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41 hmmalign Make a multiple alignment of many sequences to a common pro#le HMM.
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42
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43 Other utilities::
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44
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45 hmmconvert Convert pro#le formats to/from HMMER3 format.
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46 hmmemit Generate (sample) sequences from a pro#le HMM.
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47 hmmfetch Get a pro#le HMM by name or accession from an HMM database.
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48 hmmpress Format an HMM database into a binary format for hmmscan.
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49 hmmstat Show summary statistics for each pro#le in an HMM database
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50
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51 ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf
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52 </readme>
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53 </package>
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54
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55 </tool_dependency>
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