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